Survival Analysis
Colorectal Cancer | Ferroptosis | Unique Genes per RCD Type | Gene Expression of Tumor Samples
Mark Edward M. Gonzales1
Dr. Anish M.S. Shrestha2
I. Preliminaries
Loading libraries
library("tidyverse")
library("tibble")
library("msigdbr")
library("ggplot2")
library("TCGAbiolinks")
library("RNAseqQC")
library("DESeq2")
library("ensembldb")
library("purrr")
library("magrittr")
library("vsn")
library("matrixStats")
library("dplyr")
library("grex")
library("survminer")
library("survival")II. Downloading the TCGA gene expression data
Create a function for downloading TCGA gene expression data.
For more detailed documentation, refer to
2. Differential Gene Expression Analysis - TCGA.Rmd.
GDC_DIR = "../data/public/GDCdata"
query_and_filter_samples <- function(project) {
query_tumor <- GDCquery(
project = project,
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
experimental.strategy = "RNA-Seq",
workflow.type = "STAR - Counts",
access = "open",
sample.type = "Primary Tumor"
)
tumor <- getResults(query_tumor)
query_normal <- GDCquery(
project = project,
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
experimental.strategy = "RNA-Seq",
workflow.type = "STAR - Counts",
access = "open",
sample.type = "Solid Tissue Normal"
)
normal <- getResults(query_normal)
submitter_ids <- inner_join(tumor, normal, by = "cases.submitter_id") %>%
dplyr::select(cases.submitter_id)
tumor <- tumor %>%
dplyr::filter(cases.submitter_id %in% submitter_ids$cases.submitter_id)
normal <- normal %>%
dplyr::filter(cases.submitter_id %in% submitter_ids$cases.submitter_id)
samples <- rbind(tumor, normal)
unique(samples$sample_type)
query_project <- GDCquery(
project = project,
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
experimental.strategy = "RNA-Seq",
workflow.type = "STAR - Counts",
access = "open",
sample.type = c("Solid Tissue Normal", "Primary Tumor"),
barcode = as.list(samples$sample.submitter_id)
)
# If this is your first time running this notebook (i.e., you have not yet downloaded the results of the query in the previous block),
# uncomment the code block below
# GDCdownload(
# query_coad,
# directory = GDC_DIR
# )
return(list(samples = samples, query_project = query_project))
}Download the TCGA gene expression data for colorectal cancer (TCGA-COAD).
projects <- c("TCGA-COAD")
with_results_projects <- c()
samples <- list()
project_data <- list()
for (project in projects) {
result <- tryCatch(
{
result <- query_and_filter_samples(project)
samples[[project]] <- result$samples
project_data[[project]] <- result$query_project
with_results_projects <- c(with_results_projects, project)
},
error = function(e) {
}
)
}Running the code block above should generate and populate a directory
named GDCdata.
III. Data preprocessing
Construct the RNA-seq count matrix for each cancer type.
tcga_data <- list()
tcga_matrix <- list()
projects <- with_results_projects
for (project in projects) {
tcga_data[[project]] <- GDCprepare(
project_data[[project]],
directory = GDC_DIR,
summarizedExperiment = TRUE
)
}for (project in projects) {
count_matrix <- assay(tcga_data[[project]], "unstranded")
# Remove duplicate entries
count_matrix_df <- data.frame(count_matrix)
count_matrix_df <- count_matrix_df[!duplicated(count_matrix_df), ]
count_matrix <- data.matrix(count_matrix_df)
rownames(count_matrix) <- cleanid(rownames(count_matrix))
count_matrix <- count_matrix[!(duplicated(rownames(count_matrix)) | duplicated(rownames(count_matrix), fromLast = TRUE)), ]
tcga_matrix[[project]] <- count_matrix
}Format the samples table so that it can be fed as input
to DESeq2.
for (project in projects) {
rownames(samples[[project]]) <- samples[[project]]$cases
samples[[project]] <- samples[[project]] %>%
dplyr::select(case = "cases.submitter_id", type = "sample_type")
samples[[project]]$type <- str_replace(samples[[project]]$type, "Solid Tissue Normal", "normal")
samples[[project]]$type <- str_replace(samples[[project]]$type, "Primary Tumor", "tumor")
}DESeq2 requires the row names of samples should be
identical to the column names of count_matrix.
for (project in projects) {
colnames(tcga_matrix[[project]]) <- gsub(x = colnames(tcga_matrix[[project]]), pattern = "\\.", replacement = "-")
tcga_matrix[[project]] <- tcga_matrix[[project]][, rownames(samples[[project]])]
# Sanity check
print(all(colnames(tcga_matrix[[project]]) == rownames(samples[[project]])))
}IV. Differential gene expression analysis
For more detailed documentation on obtaining the gene set, refer to
7. Differential Gene Expression Analysis - TCGA - Pan-cancer - Unique Genes.Rmd.
RCDdb <- "../data/public/rcd-gene-list/unique-genes/necroptosis-ferroptosis-pyroptosis/"Write utility functions for filtering the gene sets, performing differential gene expression analysis, plotting the results, and performing variance-stabilizing transformation.
filter_gene_set_and_perform_dgea <- function(genes) {
tcga_rcd <- list()
for (project in projects) {
rownames(genes) <- genes$gene_id
tcga_rcd[[project]] <- tcga_matrix[[project]][rownames(tcga_matrix[[project]]) %in% genes$gene_id, ]
tcga_rcd[[project]] <- tcga_rcd[[project]][, rownames(samples[[project]])]
}
dds_rcd <- list()
res_rcd <- list()
for (project in projects) {
print(project)
print("=============")
dds <- DESeqDataSetFromMatrix(
countData = tcga_rcd[[project]],
colData = samples[[project]],
design = ~type
)
dds <- filter_genes(dds, min_count = 10)
dds$type <- relevel(dds$type, ref = "normal")
dds_rcd[[project]] <- DESeq(dds)
res_rcd[[project]] <- results(dds_rcd[[project]])
}
deseq.bbl.data <- list()
for (project in projects) {
deseq.results <- res_rcd[[project]]
deseq.bbl.data[[project]] <- data.frame(
row.names = rownames(deseq.results),
baseMean = deseq.results$baseMean,
log2FoldChange = deseq.results$log2FoldChange,
lfcSE = deseq.results$lfcSE,
stat = deseq.results$stat,
pvalue = deseq.results$pvalue,
padj = deseq.results$padj,
cancer_type = project,
gene_symbol = genes[rownames(deseq.results), "gene"]
)
}
deseq.bbl.data.combined <- bind_rows(deseq.bbl.data)
deseq.bbl.data.combined <- dplyr::filter(deseq.bbl.data.combined, abs(log2FoldChange) >= 1.5 & padj < 0.05)
return(deseq.bbl.data.combined)
}plot_dgea <- function(deseq.bbl.data.combined) {
sizes <- c("<10^-15" = 4, "10^-10" = 3, "10^-5" = 2, "0.05" = 1)
deseq.bbl.data.combined <- deseq.bbl.data.combined %>%
mutate(fdr_category = cut(padj,
breaks = c(-Inf, 1e-15, 1e-10, 1e-5, 0.05),
labels = c("<10^-15", "10^-10", "10^-5", "0.05"),
right = FALSE
))
top_genes <- deseq.bbl.data.combined %>%
group_by(cancer_type) %>%
mutate(rank = rank(-abs(log2FoldChange))) %>%
dplyr::filter(rank <= 10) %>%
ungroup()
ggplot(top_genes, aes(y = cancer_type, x = gene_symbol, size = fdr_category, fill = log2FoldChange)) +
geom_point(alpha = 0.5, shape = 21, color = "black") +
scale_size_manual(values = sizes) +
scale_fill_gradient2(low = "blue", mid = "white", high = "red", limits = c(min(deseq.bbl.data.combined$log2FoldChange), max(deseq.bbl.data.combined$log2FoldChange))) +
theme_minimal() +
theme(
axis.text.x = element_text(size = 9, angle = 90, hjust = 1)
) +
theme(legend.position = "bottom") +
theme(legend.position = "bottom") +
labs(size = "Adjusted p-value", fill = "log2 FC", y = "Cancer type", x = "Gene")
}perform_vsd <- function(genes) {
tcga_rcd <- list()
for (project in projects) {
rownames(genes) <- genes$gene_id
tcga_rcd[[project]] <- tcga_matrix[[project]][rownames(tcga_matrix[[project]]) %in% genes$gene_id, ]
tcga_rcd[[project]] <- tcga_rcd[[project]][, rownames(samples[[project]])]
}
vsd_rcd <- list()
for (project in projects) {
print(project)
print("=============")
dds <- DESeqDataSetFromMatrix(
countData = tcga_rcd[[project]],
colData = samples[[project]],
design = ~type
)
dds <- filter_genes(dds, min_count = 10)
# Perform variance stabilization
dds <- estimateSizeFactors(dds)
nsub <- sum(rowMeans(counts(dds, normalized = TRUE)) > 10)
vsd <- vst(dds, nsub = nsub)
vsd_rcd[[project]] <- assay(vsd)
}
return(vsd_rcd)
}Ferroptosis
Fetch the gene set of interest.
genes <- read.csv(paste0(RCDdb, "Ferroptosis.csv"))
print(genes)genes$gene_id <- cleanid(genes$gene_id)
genes <- distinct(genes, gene_id, .keep_all = TRUE)
genes <- subset(genes, gene_id != "")
genesFilter the genes to include only those in the gene set of interest, and then perform differential gene expression analysis.
deseq.bbl.data.combined <- filter_gene_set_and_perform_dgea(genes)[1] "TCGA-COAD"
[1] "============="Warning: some variables in design formula are characters, converting to factorsestimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
-- replacing outliers and refitting for 21 genes
-- DESeq argument 'minReplicatesForReplace' = 7
-- original counts are preserved in counts(dds)
estimating dispersions
fitting model and testingdeseq.bbl.data.combinedPlot the results.
plot_dgea(deseq.bbl.data.combined)
Perform variance-stabilizing transformation for further downstream analysis (i.e., for survival analysis).
vsd <- perform_vsd(genes)[1] "TCGA-COAD"
[1] "============="V. Downloading the clinical data
Download clinical data from TCGA, and perform some preprocessing: -
The deceased column should be FALSE if the
patient is alive and TRUE otherwise - The
overall_survival column should reflect the follow-up time
if the patient is alive and the days to death otherwise
download_clinical_data <- function(project) {
clinical_data <- GDCquery_clinic(project)
clinical_data$deceased <- ifelse(clinical_data$vital_status == "Alive", FALSE, TRUE)
clinical_data$overall_survival <- ifelse(clinical_data$vital_status == "Alive",
clinical_data$days_to_last_follow_up,
clinical_data$days_to_death
)
return(clinical_data)
}tcga_clinical <- list()
for (project in projects) {
tcga_clinical[[project]] <- download_clinical_data(project)
}VI. Performing survival analysis
Write utility functions for performing survival analysis.
construct_gene_df <- function(gene_of_interest, project) {
gene_df <- vsd[[project]] %>%
as.data.frame() %>%
rownames_to_column(var = "gene_id") %>%
gather(key = "case_id", value = "counts", -gene_id) %>%
left_join(., genes, by = "gene_id") %>%
dplyr::filter(gene == gene_of_interest) %>%
dplyr::filter(case_id %in% rownames(samples[[project]] %>% dplyr::filter(type == "tumor")))
q1 <- quantile(gene_df$counts, probs = 0.25)
q3 <- quantile(gene_df$counts, probs = 0.75)
gene_df$strata <- ifelse(gene_df$counts >= q3, "HIGH", ifelse(gene_df$counts <= q1, "LOW", "MIDDLE"))
gene_df <- gene_df %>% dplyr::filter(strata %in% c("LOW", "HIGH"))
gene_df$case_id <- paste0(sapply(strsplit(as.character(gene_df$case_id), "-"), `[`, 1), '-',
sapply(strsplit(as.character(gene_df$case_id), "-"), `[`, 2), '-',
sapply(strsplit(as.character(gene_df$case_id), "-"), `[`, 3))
gene_df <- merge(gene_df, tcga_clinical[[project]], by.x = "case_id", by.y = "submitter_id")
return(gene_df)
}compute_surival_fit <- function(gene_df) {
return (survfit(Surv(overall_survival, deceased) ~ strata, data = gene_df))
}compute_cox <- function(gene_df) {
return (coxph(Surv(overall_survival, deceased) ~ strata, data=gene_df))
}plot_survival <- function(fit) {
return(ggsurvplot(fit,
data = gene_df,
pval = T,
risk.table = T,
risk.table.height = 0.3
))
}compute_survival_diff <- function(gene_df) {
return(survdiff(Surv(overall_survival, deceased) ~ strata, data = gene_df))
}Perform survival analysis by testing for the difference in the Kaplan-Meier curves using the G-rho family of Harrington and Fleming tests: https://rdrr.io/cran/survival/man/survdiff.html
significant_projects <- c()
significant_genes <- c()
ctr <- 1
for (project in projects) {
for (gene in c(genes$gene)) {
cat(project, gene, "\n\n")
error <- tryCatch (
{
gene_df <- construct_gene_df(gene, project)
},
error = function(e) {
cat("\n\n============================\n\n")
e
}
)
if(inherits(error, "error")) next
if (nrow(gene_df) > 0) {
fit <- compute_surival_fit(gene_df)
tryCatch (
{
survival <- compute_survival_diff(gene_df)
cox <- compute_cox(gene_df)
print(ctr)
ctr <- ctr + 1
print(survival)
cat("\n")
print(cox)
print(plot_survival(fit))
if (pchisq(survival$chisq, length(survival$n)-1, lower.tail = FALSE) < 0.05) {
significant_projects <- c(significant_projects, project)
significant_genes <- c(significant_genes, gene)
}
},
error = function(e) {
}
)
}
cat("\n\n============================\n\n")
}
}TCGA-COAD MIR212
============================
TCGA-COAD NR5A2
[1] 1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.367 1.0939 1.34
strata=LOW 5 5 5.633 0.0712 1.34
Chisq= 1.3 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.4979 0.2236 1.4164 -1.058 0.29
Likelihood ratio test=1.03 on 1 df, p=0.3107
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD TFAM
============================
TCGA-COAD CREB5
[1] 2
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 1.08 0.00641 0.0105
strata=LOW 3 3 2.92 0.00238 0.0105
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1285 1.1372 1.2535 0.103 0.918
Likelihood ratio test=0.01 on 1 df, p=0.9178
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD NOS2
[1] 3
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.07 0.371 1.18
strata=LOW 3 3 1.93 0.589 1.18
Chisq= 1.2 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.208 3.348 1.173 1.03 0.303
Likelihood ratio test=1.23 on 1 df, p=0.2675
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD HULC
[1] 4
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.07 0.00215 0.00375
strata=LOW 4 4 3.93 0.00113 0.00375
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.05656 1.05819 0.92349 0.061 0.951
Likelihood ratio test=0 on 1 df, p=0.9511
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PLXNB2
[1] 5
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=2, 22 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.5 0.500 1
strata=LOW 1 1 1.5 0.167 1
Chisq= 1 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.120e+01 6.190e-10 4.019e+04 -0.001 1
Likelihood ratio test=1.39 on 1 df, p=0.239
n= 2, number of events= 2
(22 observations deleted due to missingness)
============================
TCGA-COAD KIF20A
[1] 6
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.27 0.376 1.67
strata=LOW 3 3 1.73 0.926 1.67
Chisq= 1.7 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.394 4.033 1.164 1.198 0.231
Likelihood ratio test=1.69 on 1 df, p=0.1937
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD TIMP1
============================
TCGA-COAD MIR615
============================
TCGA-COAD MIR93
============================
TCGA-COAD ENO3
[1] 7
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.59 0.451 2.82
strata=LOW 3 3 1.41 1.786 2.82
Chisq= 2.8 on 1 degrees of freedom, p= 0.09
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.744 5.719 1.166 1.496 0.135
Likelihood ratio test=2.68 on 1 df, p=0.1015
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MMD
[1] 8
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.2 0.345 0.871
strata=LOW 5 5 3.8 0.382 0.871
Chisq= 0.9 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.7793 2.1799 0.8539 0.913 0.361
Likelihood ratio test=0.91 on 1 df, p=0.3407
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD NQO1
[1] 9
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MARCHF5
[1] 10
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.98 0.521 0.899
strata=LOW 3 3 4.02 0.257 0.899
Chisq= 0.9 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.8606 0.4229 0.9325 -0.923 0.356
Likelihood ratio test=0.87 on 1 df, p=0.3496
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD JUN
[1] 11
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.14 0.00357 0.0104
strata=LOW 4 4 3.86 0.00474 0.0104
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.07581 1.07876 0.74513 0.102 0.919
Likelihood ratio test=0.01 on 1 df, p=0.9192
n= 9, number of events= 9
(15 observations deleted due to missingness)
============================
TCGA-COAD ALDH3A2
[1] 12
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.19 0.00722 0.0192
strata=LOW 4 4 3.81 0.00985 0.0192
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.09896 1.10402 0.71460 0.138 0.89
Likelihood ratio test=0.02 on 1 df, p=0.8899
n= 9, number of events= 9
(15 observations deleted due to missingness)
============================
TCGA-COAD ALOX5
============================
TCGA-COAD PARP9
[1] 13
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.23 0.0168 0.0449
strata=LOW 3 3 2.77 0.0197 0.0449
Chisq= 0 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1950 1.2153 0.9213 0.212 0.832
Likelihood ratio test=0.05 on 1 df, p=0.8315
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD GLRX5
[1] 14
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=2, 22 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.5 0.500 1
strata=LOW 1 1 1.5 0.167 1
Chisq= 1 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.120e+01 6.190e-10 4.019e+04 -0.001 1
Likelihood ratio test=1.39 on 1 df, p=0.239
n= 2, number of events= 2
(22 observations deleted due to missingness)
============================
TCGA-COAD METTL14
[1] 15
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 2.08 0.563 1.78
strata=LOW 3 3 1.92 0.612 1.78
Chisq= 1.8 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.085e+01 1.136e+09 2.490e+04 0.001 0.999
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD TOR2A
[1] 16
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.52 0.0928 0.26
strata=LOW 2 2 2.48 0.0941 0.26
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5892 0.5548 1.1718 -0.503 0.615
Likelihood ratio test=0.27 on 1 df, p=0.6001
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PARP14
[1] 17
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.82 0.237 0.594
strata=LOW 4 4 3.18 0.210 0.594
Chisq= 0.6 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.8475 2.3338 1.1303 0.75 0.453
Likelihood ratio test=0.65 on 1 df, p=0.4198
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR130B
============================
TCGA-COAD CERS6-AS1
============================
TCGA-COAD NFS1
[1] 18
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.07 0.00215 0.00462
strata=LOW 3 3 2.93 0.00152 0.00462
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.06924 1.07170 1.01903 0.068 0.946
Likelihood ratio test=0 on 1 df, p=0.9458
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD SLC3A2
[1] 19
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=2, 22 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.5 0.500 1
strata=LOW 1 1 1.5 0.167 1
Chisq= 1 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.120e+01 6.190e-10 4.019e+04 -0.001 1
Likelihood ratio test=1.39 on 1 df, p=0.239
n= 2, number of events= 2
(22 observations deleted due to missingness)
============================
TCGA-COAD ZFAS1
[1] 20
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.2 0.0119 0.0262
strata=LOW 4 4 3.8 0.0100 0.0262
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1336 1.1430 0.8268 0.162 0.872
Likelihood ratio test=0.03 on 1 df, p=0.8716
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD PANX1
[1] 21
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.43 0.0424 0.201
strata=LOW 2 2 1.57 0.1199 0.201
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4492 1.5670 1.0100 0.445 0.657
Likelihood ratio test=0.2 on 1 df, p=0.6578
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD HSPB1
[1] 22
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 3.9 0.312 0.916
strata=LOW 2 2 3.1 0.392 0.916
Chisq= 0.9 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.0172 0.3616 1.1061 -0.92 0.358
Likelihood ratio test=1.03 on 1 df, p=0.3097
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD CREB1
[1] 23
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 2.28 0.721 2.01
strata=LOW 4 4 2.72 0.606 2.01
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.077e+01 1.049e+09 2.244e+04 0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD EZH2
[1] 24
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.57 0.688 3.45
strata=LOW 3 3 1.43 1.712 3.45
Chisq= 3.4 on 1 degrees of freedom, p= 0.06
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.144e+01 2.040e+09 2.359e+04 0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD SLC40A1
[1] 25
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.85 0.01176 0.0191
strata=LOW 5 5 5.15 0.00423 0.0191
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1278 0.8801 0.9241 -0.138 0.89
Likelihood ratio test=0.02 on 1 df, p=0.8905
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD PAQR3
[1] 26
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.57 0.090 0.265
strata=LOW 3 3 2.43 0.132 0.265
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4730 1.6048 0.9269 0.51 0.61
Likelihood ratio test=0.27 on 1 df, p=0.6059
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR545
============================
TCGA-COAD MIR6077
============================
TCGA-COAD MIR424
============================
TCGA-COAD NOX5
[1] 27
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.017 0.257 1.59
strata=LOW 2 2 0.983 1.051 1.59
Chisq= 1.6 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.439 4.215 1.236 1.164 0.244
Likelihood ratio test=1.46 on 1 df, p=0.2262
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD DHODH
[1] 28
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4 5.66e-06 1.56e-05
strata=LOW 3 3 3 7.57e-06 1.56e-05
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.003268 1.003273 0.828416 0.004 0.997
Likelihood ratio test=0 on 1 df, p=0.9969
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD PTPN18
[1] 29
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.27 0.376 1.67
strata=LOW 3 3 1.73 0.926 1.67
Chisq= 1.7 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.394 4.033 1.164 1.198 0.231
Likelihood ratio test=1.69 on 1 df, p=0.1937
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD IARS1
[1] 30
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.45 0.388 2.04
strata=LOW 3 3 1.55 1.370 2.04
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.2510 3.4940 0.9283 1.348 0.178
Likelihood ratio test=1.85 on 1 df, p=0.1734
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD IL4R
[1] 31
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.93 0.00113 0.00375
strata=LOW 2 2 2.07 0.00215 0.00375
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.05656 0.94501 0.92349 -0.061 0.951
Likelihood ratio test=0 on 1 df, p=0.9511
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD SENP1
[1] 32
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 1.83 0.379 1.47
strata=LOW 2 2 1.17 0.595 1.47
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.097e+01 1.286e+09 2.928e+04 0.001 0.999
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD IFNA16
============================
TCGA-COAD SOX2
[1] 33
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.77 0.0197 0.0449
strata=LOW 3 3 3.23 0.0168 0.0449
Chisq= 0 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1950 0.8229 0.9213 -0.212 0.832
Likelihood ratio test=0.05 on 1 df, p=0.8315
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD LIFR
[1] 34
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.05 0.446 0.708
strata=LOW 4 4 4.95 0.184 0.708
Chisq= 0.7 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.6931 0.5000 0.8379 -0.827 0.408
Likelihood ratio test=0.67 on 1 df, p=0.412
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR199A2
============================
TCGA-COAD COX4I2
[1] 35
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.55 0.0665 0.871
strata=LOW 1 1 0.45 0.6722 0.871
Chisq= 0.9 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.242 3.464 1.418 0.876 0.381
Likelihood ratio test=0.72 on 1 df, p=0.395
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD ATF2
[1] 36
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.25 2.25 3
strata=LOW 3 3 3.75 0.15 3
Chisq= 3 on 1 degrees of freedom, p= 0.08
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.208e+01 2.562e-10 3.607e+04 -0.001 1
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD ABCC5
[1] 37
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.57 0.1199 0.201
strata=LOW 4 4 4.43 0.0424 0.201
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.4492 0.6381 1.0100 -0.445 0.657
Likelihood ratio test=0.2 on 1 df, p=0.6578
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD CCDC6
[1] 38
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.7 0.617 2.05
strata=LOW 5 5 3.3 0.880 2.05
Chisq= 2.1 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.478 4.383 1.116 1.325 0.185
Likelihood ratio test=2.29 on 1 df, p=0.1306
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD OTUB1
[1] 39
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.667 0.167 2
strata=LOW 1 1 0.333 1.333 2
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.215e+01 4.171e+09 4.566e+04 0 1
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD ALOXE3
[1] 40
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.83 0.118 0.367
strata=LOW 4 4 3.17 0.216 0.367
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4304 1.5379 0.7158 0.601 0.548
Likelihood ratio test=0.36 on 1 df, p=0.5491
n= 9, number of events= 9
(15 observations deleted due to missingness)
============================
TCGA-COAD SCP2
[1] 41
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.77 0.156 0.825
strata=LOW 2 2 1.23 0.477 0.825
Chisq= 0.8 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.073 2.924 1.235 0.869 0.385
Likelihood ratio test=0.81 on 1 df, p=0.3677
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PHKG2
[1] 42
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.02 9.21e-05 0.000242
strata=LOW 3 3 2.98 9.31e-05 0.000242
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.01448 1.01458 0.93137 0.016 0.988
Likelihood ratio test=0 on 1 df, p=0.9876
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MTDH
[1] 43
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.62 0.0909 0.141
strata=LOW 4 4 4.38 0.0335 0.141
Chisq= 0.1 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.3503 0.7045 0.9368 -0.374 0.708
Likelihood ratio test=0.14 on 1 df, p=0.712
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD ACO1
[1] 44
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.333 1.333 2
strata=LOW 2 2 2.667 0.167 2
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.215e+01 2.398e-10 4.566e+04 0 1
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD MIR137
============================
TCGA-COAD OIP5-AS1
[1] 45
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MIR494
============================
TCGA-COAD MLLT1
[1] 46
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.43 0.132 0.265
strata=LOW 3 3 3.57 0.090 0.265
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.4730 0.6231 0.9269 -0.51 0.61
Likelihood ratio test=0.27 on 1 df, p=0.6059
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR19B1
============================
TCGA-COAD RPTOR
[1] 47
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.017 0.257 1.59
strata=LOW 2 2 0.983 1.051 1.59
Chisq= 1.6 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.439 4.215 1.236 1.164 0.244
Likelihood ratio test=1.46 on 1 df, p=0.2262
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD GCH1
[1] 48
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.4 0.0293 0.147
strata=LOW 2 2 1.6 0.0987 0.147
Chisq= 0.1 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.3505 1.4197 0.9188 0.381 0.703
Likelihood ratio test=0.14 on 1 df, p=0.7067
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD PARP16
[1] 49
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.95 0.765 3.31
strata=LOW 4 4 2.05 1.842 3.31
Chisq= 3.3 on 1 degrees of freedom, p= 0.07
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.840 6.294 1.139 1.615 0.106
Likelihood ratio test=3.35 on 1 df, p=0.06722
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR9-3
============================
TCGA-COAD CISD3
[1] 50
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.02 9.21e-05 0.000242
strata=LOW 3 3 2.98 9.31e-05 0.000242
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.01448 1.01458 0.93137 0.016 0.988
Likelihood ratio test=0 on 1 df, p=0.9876
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD USP35
[1] 51
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.32 0.3546 0.536
strata=LOW 4 4 4.68 0.0997 0.536
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7222 0.4857 1.0075 -0.717 0.474
Likelihood ratio test=0.5 on 1 df, p=0.478
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PRKAA1
[1] 52
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 1.28 0.0626 0.0979
strata=LOW 4 4 3.72 0.0216 0.0979
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.3695 1.4470 1.1865 0.311 0.755
Likelihood ratio test=0.1 on 1 df, p=0.7492
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MAPK14
============================
TCGA-COAD GRIA3
[1] 53
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3 0.330 0.68
strata=LOW 3 3 4 0.248 0.68
Chisq= 0.7 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7106 0.4913 0.8786 -0.809 0.419
Likelihood ratio test=0.69 on 1 df, p=0.405
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD KDM5C
[1] 54
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.52 0.1523 0.222
strata=LOW 6 6 6.48 0.0357 0.222
Chisq= 0.2 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.4308 0.6500 0.9207 -0.468 0.64
Likelihood ratio test=0.21 on 1 df, p=0.6456
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD DECR1
[1] 55
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.68 0.0997 0.536
strata=LOW 2 2 1.32 0.3546 0.536
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.7222 2.0589 1.0075 0.717 0.474
Likelihood ratio test=0.5 on 1 df, p=0.478
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD VCP
[1] 56
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.93 0.589 1.18
strata=LOW 2 2 3.07 0.371 1.18
Chisq= 1.2 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.2084 0.2987 1.1730 -1.03 0.303
Likelihood ratio test=1.23 on 1 df, p=0.2675
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MIR129-1
============================
TCGA-COAD PARP10
[1] 57
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.417 0.0508 0.424
strata=LOW 1 1 0.583 0.2976 0.424
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.8959 2.4495 1.4215 0.63 0.529
Likelihood ratio test=0.38 on 1 df, p=0.535
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD ULK2
[1] 58
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.25 2.25 3
strata=LOW 3 3 3.75 0.15 3
Chisq= 3 on 1 degrees of freedom, p= 0.08
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.208e+01 2.562e-10 3.607e+04 -0.001 1
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD CISD1
[1] 59
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 1.08 0.00641 0.0105
strata=LOW 3 3 2.92 0.00238 0.0105
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1285 1.1372 1.2535 0.103 0.918
Likelihood ratio test=0.01 on 1 df, p=0.9178
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD MIR147A
============================
TCGA-COAD BBOX1-AS1
[1] 60
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.42 0.373 2.19
strata=LOW 3 3 1.58 1.280 2.19
Chisq= 2.2 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.586 4.883 1.174 1.35 0.177
Likelihood ratio test=2.17 on 1 df, p=0.1411
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD RB1
[1] 61
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.25 2.25 3
strata=LOW 3 3 3.75 0.15 3
Chisq= 3 on 1 degrees of freedom, p= 0.08
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.208e+01 2.562e-10 3.607e+04 -0.001 1
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD TTPA
[1] 62
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.367 1.0939 1.34
strata=LOW 5 5 5.633 0.0712 1.34
Chisq= 1.3 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.4979 0.2236 1.4164 -1.058 0.29
Likelihood ratio test=1.03 on 1 df, p=0.3107
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD CDC25A
[1] 63
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.417 0.0508 0.424
strata=LOW 1 1 0.583 0.2976 0.424
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.8959 2.4495 1.4215 0.63 0.529
Likelihood ratio test=0.38 on 1 df, p=0.535
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD PCAT1
[1] 64
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.95 0.002632 0.00353
strata=LOW 5 5 5.05 0.000495 0.00353
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.06936 0.93299 1.16790 -0.059 0.953
Likelihood ratio test=0 on 1 df, p=0.9529
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD DAZAP1
[1] 65
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.217 0.284 2.6
strata=LOW 2 2 0.783 1.890 2.6
Chisq= 2.6 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.766 5.849 1.235 1.43 0.153
Likelihood ratio test=2.2 on 1 df, p=0.1382
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PEX2
[1] 66
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.23 0.263 0.485
strata=LOW 3 3 3.77 0.156 0.485
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.6321 0.5315 0.9220 -0.686 0.493
Likelihood ratio test=0.48 on 1 df, p=0.4874
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR124-3
============================
TCGA-COAD TRIM21
[1] 67
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.45 0.470 1.5
strata=LOW 4 4 2.55 0.818 1.5
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.046 2.845 0.888 1.178 0.239
Likelihood ratio test=1.49 on 1 df, p=0.2226
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MEG3
[1] 68
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.23 0.263 0.485
strata=LOW 3 3 3.77 0.156 0.485
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.6321 0.5315 0.9220 -0.686 0.493
Likelihood ratio test=0.48 on 1 df, p=0.4874
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD GCLC
[1] 69
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 1.83 0.379 1.47
strata=LOW 2 2 1.17 0.595 1.47
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.097e+01 1.286e+09 2.928e+04 0.001 0.999
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD IDH2
[1] 70
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.9 0.926 3.86
strata=LOW 4 4 2.1 1.719 3.86
Chisq= 3.9 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.129e+01 1.754e+09 2.052e+04 0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD FNDC5
[1] 71
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.45 0.0575 0.142
strata=LOW 4 4 3.55 0.0558 0.142
Chisq= 0.1 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.3150 1.3703 0.8385 0.376 0.707
Likelihood ratio test=0.14 on 1 df, p=0.7076
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD FANCD2
[1] 72
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 1.83 0.379 1.47
strata=LOW 2 2 1.17 0.595 1.47
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.097e+01 1.286e+09 2.928e+04 0.001 0.999
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD LCN2
[1] 73
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.1 1.719 3.86
strata=LOW 2 2 3.9 0.926 3.86
Chisq= 3.9 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.129e+01 5.700e-10 2.052e+04 -0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD TFR2
[1] 74
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.77 0.156 0.485
strata=LOW 3 3 2.23 0.263 0.485
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.6321 1.8815 0.9220 0.686 0.493
Likelihood ratio test=0.48 on 1 df, p=0.4874
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PARP12
[1] 75
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.82 0.237 0.594
strata=LOW 4 4 3.18 0.210 0.594
Chisq= 0.6 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.8475 2.3338 1.1303 0.75 0.453
Likelihood ratio test=0.65 on 1 df, p=0.4198
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD NR1D1
[1] 76
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 6.348 0.286 3.61
strata=LOW 2 2 0.652 2.784 3.61
Chisq= 3.6 on 1 degrees of freedom, p= 0.06
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.012 7.475 1.236 1.628 0.104
Likelihood ratio test=2.83 on 1 df, p=0.09274
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD ATG13
[1] 77
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.167 0.0128 0.0588
strata=LOW 1 1 0.833 0.0333 0.0588
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.3466 1.4142 1.4355 0.241 0.809
Likelihood ratio test=0.06 on 1 df, p=0.8096
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD TMSB4X
[1] 78
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.17 0.595 1.47
strata=LOW 1 1 1.83 0.379 1.47
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.097e+01 7.775e-10 2.928e+04 -0.001 0.999
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD CDK14
[1] 79
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.92 0.00238 0.0105
strata=LOW 1 1 1.08 0.00641 0.0105
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1285 0.8794 1.2535 -0.103 0.918
Likelihood ratio test=0.01 on 1 df, p=0.9178
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD RP1-228H13.5
[1] 80
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.33 0.408 1.5
strata=LOW 4 4 2.67 0.661 1.5
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.313 3.719 1.141 1.151 0.25
Likelihood ratio test=1.62 on 1 df, p=0.2028
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD NOX3
============================
TCGA-COAD IFNA17
============================
TCGA-COAD ALOX12B
[1] 81
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.07 0.280 1.18
strata=LOW 3 3 1.93 0.589 1.18
Chisq= 1.2 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.208 3.348 1.173 1.03 0.303
Likelihood ratio test=1.23 on 1 df, p=0.2675
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PGRMC1
[1] 82
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.2 0.0119 0.0262
strata=LOW 4 4 3.8 0.0100 0.0262
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1336 1.1430 0.8268 0.162 0.872
Likelihood ratio test=0.03 on 1 df, p=0.8716
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD ULK1
[1] 83
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.417 0.0508 0.424
strata=LOW 1 1 0.583 0.2976 0.424
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.8959 2.4495 1.4215 0.63 0.529
Likelihood ratio test=0.38 on 1 df, p=0.535
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD TRIM26
[1] 84
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.017 0.257 1.59
strata=LOW 2 2 0.983 1.051 1.59
Chisq= 1.6 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.439 4.215 1.236 1.164 0.244
Likelihood ratio test=1.46 on 1 df, p=0.2262
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD QSOX1
[1] 85
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.93 0.589 1.18
strata=LOW 3 3 4.07 0.280 1.18
Chisq= 1.2 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.2084 0.2987 1.1730 -1.03 0.303
Likelihood ratio test=1.23 on 1 df, p=0.2675
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD ATM
[1] 86
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.452 5.294 6.98
strata=LOW 5 5 6.548 0.366 6.98
Chisq= 7 on 1 degrees of freedom, p= 0.008
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.158e+01 4.233e-10 1.775e+04 -0.001 0.999
Likelihood ratio test=6.09 on 1 df, p=0.0136
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIB2
[1] 87
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.217 0.284 2.6
strata=LOW 2 2 0.783 1.890 2.6
Chisq= 2.6 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.766 5.849 1.235 1.43 0.153
Likelihood ratio test=2.2 on 1 df, p=0.1382
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD SLC1A5
[1] 88
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.1 0.199 0.654
strata=LOW 2 2 2.9 0.281 0.654
Chisq= 0.7 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.8731 0.4177 1.1117 -0.785 0.432
Likelihood ratio test=0.73 on 1 df, p=0.3923
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR2115
============================
TCGA-COAD LINC00336
[1] 89
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.55 0.0445 0.211
strata=LOW 1 1 1.45 0.1397 0.211
Chisq= 0.2 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5241 0.5921 1.1513 -0.455 0.649
Likelihood ratio test=0.23 on 1 df, p=0.6342
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD NDRG1
[1] 90
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.467 0.393 5.63
strata=LOW 2 2 0.533 4.033 5.63
Chisq= 5.6 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.195e+01 3.399e+09 2.380e+04 0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD TAFAZZIN
[1] 91
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.52 0.0759 0.297
strata=LOW 2 2 1.48 0.1800 0.297
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.5493 1.7321 1.0198 0.539 0.59
Likelihood ratio test=0.29 on 1 df, p=0.5922
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MIR135B
============================
TCGA-COAD GLS2
[1] 92
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.9 0.165 0.453
strata=LOW 5 5 4.1 0.197 0.453
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4886 1.6300 0.7316 0.668 0.504
Likelihood ratio test=0.44 on 1 df, p=0.5058
n= 9, number of events= 9
(15 observations deleted due to missingness)
============================
TCGA-COAD HELLS
[1] 93
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.57 0.688 3.45
strata=LOW 3 3 1.43 1.712 3.45
Chisq= 3.4 on 1 degrees of freedom, p= 0.06
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.144e+01 2.040e+09 2.359e+04 0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD KLF2
[1] 94
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.72 0.0216 0.0979
strata=LOW 1 1 1.28 0.0626 0.0979
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.3695 0.6911 1.1865 -0.311 0.755
Likelihood ratio test=0.1 on 1 df, p=0.7492
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD TFAP2A
[1] 95
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.017 0.257 1.59
strata=LOW 2 2 0.983 1.051 1.59
Chisq= 1.6 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.439 4.215 1.236 1.164 0.244
Likelihood ratio test=1.46 on 1 df, p=0.2262
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD FURIN
[1] 96
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.333 1.333 2
strata=LOW 2 2 2.667 0.167 2
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.215e+01 2.398e-10 4.566e+04 0 1
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD CDH1
[1] 97
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.617 0.2383 0.302
strata=LOW 5 5 5.383 0.0273 0.302
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.6644 0.5146 1.2307 -0.54 0.589
Likelihood ratio test=0.27 on 1 df, p=0.6049
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR6852
============================
TCGA-COAD MIR670
============================
TCGA-COAD TYRO3
[1] 98
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 2.08 0.563 1.78
strata=LOW 3 3 1.92 0.612 1.78
Chisq= 1.8 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.085e+01 1.136e+09 2.490e+04 0.001 0.999
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD MIR4715
============================
TCGA-COAD ABHD12
[1] 99
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.67 0.0667 0.154
strata=LOW 2 2 2.33 0.0476 0.154
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.4812 0.6180 1.2380 -0.389 0.697
Likelihood ratio test=0.16 on 1 df, p=0.6913
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD ATG7
[1] 100
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.7 0.612 2.38
strata=LOW 4 4 2.3 1.247 2.38
Chisq= 2.4 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.584 4.875 1.129 1.403 0.161
Likelihood ratio test=2.5 on 1 df, p=0.1141
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MT1G
[1] 101
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.45 0.6722 0.871
strata=LOW 4 4 4.55 0.0665 0.871
Chisq= 0.9 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.2425 0.2887 1.4179 -0.876 0.381
Likelihood ratio test=0.72 on 1 df, p=0.395
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD SAT1
[1] 102
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.23 0.477 0.825
strata=LOW 3 3 3.77 0.156 0.825
Chisq= 0.8 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.073 0.342 1.235 -0.869 0.385
Likelihood ratio test=0.81 on 1 df, p=0.3677
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MIR182
============================
TCGA-COAD HOTAIR
[1] 103
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.89 0.606 2.18
strata=LOW 5 5 3.11 1.148 2.18
Chisq= 2.2 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.2023 3.3279 0.8576 1.402 0.161
Likelihood ratio test=2.2 on 1 df, p=0.1379
n= 9, number of events= 9
(19 observations deleted due to missingness)
============================
TCGA-COAD PIR
[1] 104
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.52 0.0928 0.26
strata=LOW 2 2 2.48 0.0941 0.26
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5892 0.5548 1.1718 -0.503 0.615
Likelihood ratio test=0.27 on 1 df, p=0.6001
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD ELAVL1
[1] 105
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5 0.202 0.856
strata=LOW 3 3 2 0.506 0.856
Chisq= 0.9 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.8286 2.2902 0.9202 0.901 0.368
Likelihood ratio test=0.83 on 1 df, p=0.3615
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD ACADSB
[1] 106
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 2.08 0.563 1.78
strata=LOW 3 3 1.92 0.612 1.78
Chisq= 1.8 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.085e+01 1.136e+09 2.490e+04 0.001 0.999
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD NCOA4
============================
TCGA-COAD IFNA10
============================
TCGA-COAD IFNA13
============================
TCGA-COAD MIR9-2
============================
TCGA-COAD RRM2
[1] 107
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.66 0.120 0.301
strata=LOW 4 4 3.34 0.131 0.301
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4740 1.6063 0.8721 0.543 0.587
Likelihood ratio test=0.31 on 1 df, p=0.5787
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD EPSTI1
[1] 108
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.16 0.00630 0.0154
strata=LOW 4 4 3.84 0.00683 0.0154
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.09533 1.10002 0.76955 0.124 0.901
Likelihood ratio test=0.02 on 1 df, p=0.9012
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD LINC00551
[1] 109
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD SLC25A28
[1] 110
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.417 0.0508 0.424
strata=LOW 1 1 0.583 0.2976 0.424
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.8959 2.4495 1.4215 0.63 0.529
Likelihood ratio test=0.38 on 1 df, p=0.535
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD LINC00973
============================
TCGA-COAD MIR378A
============================
TCGA-COAD MGST1
[1] 111
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.15 0.00423 0.0191
strata=LOW 2 2 1.85 0.01176 0.0191
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1278 1.1363 0.9241 0.138 0.89
Likelihood ratio test=0.02 on 1 df, p=0.8905
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIB1
[1] 112
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD SRC
[1] 113
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.93 0.589 1.18
strata=LOW 2 2 3.07 0.371 1.18
Chisq= 1.2 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.2084 0.2987 1.1730 -1.03 0.303
Likelihood ratio test=1.23 on 1 df, p=0.2675
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD ATG5
============================
TCGA-COAD ACVR1B
[1] 114
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.83 0.01039 0.0206
strata=LOW 4 4 4.17 0.00705 0.0206
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1196 0.8872 0.8348 -0.143 0.886
Likelihood ratio test=0.02 on 1 df, p=0.8861
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD NT5DC2
[1] 115
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.52 0.0759 0.297
strata=LOW 2 2 1.48 0.1800 0.297
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.5493 1.7321 1.0198 0.539 0.59
Likelihood ratio test=0.29 on 1 df, p=0.5922
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PIK3CA
[1] 116
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.33 0.0476 0.154
strata=LOW 2 2 1.67 0.0667 0.154
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4812 1.6180 1.2380 0.389 0.697
Likelihood ratio test=0.16 on 1 df, p=0.6913
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD NUPR1
[1] 117
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.52 0.0928 0.26
strata=LOW 2 2 2.48 0.0941 0.26
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5892 0.5548 1.1718 -0.503 0.615
Likelihood ratio test=0.27 on 1 df, p=0.6001
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD AKT1S1
[1] 118
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.8 0.133 4
strata=LOW 1 1 0.2 3.200 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.204e+01 3.739e+09 3.057e+04 0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MIR19A
============================
TCGA-COAD USP7
[1] 119
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.73 0.0273 0.0458
strata=LOW 5 5 5.27 0.0141 0.0458
Chisq= 0 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1654 0.8475 0.7738 -0.214 0.831
Likelihood ratio test=0.05 on 1 df, p=0.8314
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD TMSB4Y
[1] 120
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 23 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.25 0.0185 0.044
strata=LOW 4 4 3.75 0.0160 0.044
Chisq= 0 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1838 1.2018 0.8774 0.209 0.834
Likelihood ratio test=0.04 on 1 df, p=0.8326
n= 7, number of events= 7
(23 observations deleted due to missingness)
============================
TCGA-COAD SIAH2
[1] 121
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.95 0.000517 0.00159
strata=LOW 3 3 3.05 0.000672 0.00159
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.03534 0.96528 0.88617 -0.04 0.968
Likelihood ratio test=0 on 1 df, p=0.9681
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR29A
============================
TCGA-COAD CHAC1
[1] 122
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.43 1.712 3.45
strata=LOW 2 2 3.57 0.688 3.45
Chisq= 3.4 on 1 degrees of freedom, p= 0.06
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.144e+01 4.901e-10 2.359e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD LINC00616
[1] 123
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=12, 31 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.28 0.03380 0.0462
strata=LOW 10 10 9.72 0.00792 0.0462
Chisq= 0 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1743 1.1904 0.8119 0.215 0.83
Likelihood ratio test=0.05 on 1 df, p=0.8273
n= 12, number of events= 12
(31 observations deleted due to missingness)
============================
TCGA-COAD PRKAA2
[1] 124
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.452 5.294 6.98
strata=LOW 5 5 6.548 0.366 6.98
Chisq= 7 on 1 degrees of freedom, p= 0.008
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.158e+01 4.233e-10 1.775e+04 -0.001 0.999
Likelihood ratio test=6.09 on 1 df, p=0.0136
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD LONP1
[1] 125
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.35 0.419 4.26
strata=LOW 2 2 0.65 2.804 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.232e+01 4.923e+09 3.308e+04 0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PPARG
[1] 126
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.23 0.477 0.825
strata=LOW 3 3 3.77 0.156 0.825
Chisq= 0.8 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.073 0.342 1.235 -0.869 0.385
Likelihood ratio test=0.81 on 1 df, p=0.3677
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MAPK1
[1] 127
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.2 3.200 4
strata=LOW 4 4 4.8 0.133 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.204e+01 2.674e-10 3.057e+04 -0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PEX6
[1] 128
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.27 0.4210 0.626
strata=LOW 5 5 5.73 0.0932 0.626
Chisq= 0.6 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7787 0.4590 1.0083 -0.772 0.44
Likelihood ratio test=0.58 on 1 df, p=0.4453
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD PPARA
[1] 129
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.81 0.135 0.333
strata=LOW 5 5 4.19 0.155 0.333
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4224 1.5256 0.7374 0.573 0.567
Likelihood ratio test=0.34 on 1 df, p=0.5615
n= 9, number of events= 9
(15 observations deleted due to missingness)
============================
TCGA-COAD ACSL4
[1] 130
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.69 0.771 2.05
strata=LOW 5 5 3.31 0.857 2.05
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.481 4.399 1.119 1.324 0.185
Likelihood ratio test=2.27 on 1 df, p=0.1317
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD ANO6
[1] 131
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.07 0.371 1.18
strata=LOW 3 3 1.93 0.589 1.18
Chisq= 1.2 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.208 3.348 1.173 1.03 0.303
Likelihood ratio test=1.23 on 1 df, p=0.2675
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD YTHDC2
[1] 132
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 4.19 1.14 4.2
strata=LOW 5 5 2.81 1.70 4.2
Chisq= 4.2 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.118e+01 1.579e+09 1.860e+04 0.001 0.999
Likelihood ratio test=6.09 on 1 df, p=0.0136
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR103A1
============================
TCGA-COAD INTS2
[1] 133
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 2.08 0.563 1.78
strata=LOW 3 3 1.92 0.612 1.78
Chisq= 1.8 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.085e+01 1.136e+09 2.490e+04 0.001 0.999
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD PTPN6
[1] 134
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.55 0.0665 0.871
strata=LOW 1 1 0.45 0.6722 0.871
Chisq= 0.9 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.242 3.464 1.418 0.876 0.381
Likelihood ratio test=0.72 on 1 df, p=0.395
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD SMAD7
[1] 135
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD ATG16L1
[1] 136
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.94 0.952 2.38
strata=LOW 6 6 4.06 0.922 2.38
Chisq= 2.4 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.565 4.783 1.105 1.416 0.157
Likelihood ratio test=2.71 on 1 df, p=0.09989
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD LINC00976
[1] 137
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.83 0.01039 0.0206
strata=LOW 4 4 4.17 0.00705 0.0206
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1196 0.8872 0.8348 -0.143 0.886
Likelihood ratio test=0.02 on 1 df, p=0.8861
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD H19
[1] 138
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.73 0.0410 0.0739
strata=LOW 3 3 3.27 0.0218 0.0739
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.2739 0.7604 1.0107 -0.271 0.786
Likelihood ratio test=0.07 on 1 df, p=0.7866
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD FADS1
[1] 139
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.41 1.046 1.81
strata=LOW 4 4 5.59 0.451 1.81
Chisq= 1.8 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.1303 0.3229 0.8813 -1.283 0.2
Likelihood ratio test=1.77 on 1 df, p=0.1832
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD CHP1
[1] 140
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.43 0.132 0.265
strata=LOW 3 3 3.57 0.090 0.265
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.4730 0.6231 0.9269 -0.51 0.61
Likelihood ratio test=0.27 on 1 df, p=0.6059
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PRR5
============================
TCGA-COAD CFL1
[1] 141
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.77 0.156 0.825
strata=LOW 2 2 1.23 0.477 0.825
Chisq= 0.8 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.073 2.924 1.235 0.869 0.385
Likelihood ratio test=0.81 on 1 df, p=0.3677
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MIR382
============================
TCGA-COAD LAMP2
[1] 142
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.17 0.595 1.47
strata=LOW 1 1 1.83 0.379 1.47
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.097e+01 7.775e-10 2.928e+04 -0.001 0.999
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD PTPN14
[1] 143
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 0.962 4.318 6.62
strata=LOW 4 4 6.038 0.688 6.62
Chisq= 6.6 on 1 degrees of freedom, p= 0.01
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.242e+01 1.833e-10 2.728e+04 -0.001 0.999
Likelihood ratio test=7.11 on 1 df, p=0.007663
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD AGPAT3
[1] 144
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.07 0.371 0.961
strata=LOW 4 4 2.93 0.388 0.961
Chisq= 1 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.057 2.877 1.127 0.938 0.348
Likelihood ratio test=1.05 on 1 df, p=0.3051
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD STING1
[1] 145
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.92 0.00238 0.0105
strata=LOW 1 1 1.08 0.00641 0.0105
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1285 0.8794 1.2535 -0.103 0.918
Likelihood ratio test=0.01 on 1 df, p=0.9178
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD ABCC1
[1] 146
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.14 0.00461 0.0131
strata=LOW 3 3 2.86 0.00666 0.0131
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.09465 1.09927 0.82764 0.114 0.909
Likelihood ratio test=0.01 on 1 df, p=0.909
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD IFNA5
============================
TCGA-COAD MIR140
============================
TCGA-COAD MYB
[1] 147
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.4 0.576 1.65
strata=LOW 4 4 2.6 0.754 1.65
Chisq= 1.7 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.370 3.934 1.139 1.202 0.229
Likelihood ratio test=1.78 on 1 df, p=0.1818
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD IFNA6
============================
TCGA-COAD IFNA14
============================
TCGA-COAD BDNF-AS
[1] 148
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.4 1.070 1.83
strata=LOW 5 5 6.6 0.389 1.83
Chisq= 1.8 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.1311 0.3227 0.8782 -1.288 0.198
Likelihood ratio test=1.79 on 1 df, p=0.1811
n= 9, number of events= 9
(15 observations deleted due to missingness)
============================
TCGA-COAD TRIB2
[1] 149
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 5.9 0.00178 0.0079
strata=LOW 2 2 2.1 0.00499 0.0079
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.0781 0.9249 0.8787 -0.089 0.929
Likelihood ratio test=0.01 on 1 df, p=0.9289
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD MALAT1
[1] 150
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.617 0.2383 0.302
strata=LOW 5 5 5.383 0.0273 0.302
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.6644 0.5146 1.2307 -0.54 0.589
Likelihood ratio test=0.27 on 1 df, p=0.6049
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD FH
[1] 151
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.4 0.576 1.65
strata=LOW 4 4 2.6 0.754 1.65
Chisq= 1.7 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.370 3.934 1.139 1.202 0.229
Likelihood ratio test=1.78 on 1 df, p=0.1818
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PEX10
[1] 152
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.4 0.0667 0.135
strata=LOW 4 4 3.6 0.0444 0.135
Chisq= 0.1 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.3429 1.4090 0.9368 0.366 0.714
Likelihood ratio test=0.14 on 1 df, p=0.712
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD SCD
[1] 153
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.67 0.0667 0.154
strata=LOW 2 2 2.33 0.0476 0.154
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.4812 0.6180 1.2380 -0.389 0.697
Likelihood ratio test=0.16 on 1 df, p=0.6913
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD FTL
[1] 154
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.77 0.156 0.825
strata=LOW 2 2 1.23 0.477 0.825
Chisq= 0.8 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.073 2.924 1.235 0.869 0.385
Likelihood ratio test=0.81 on 1 df, p=0.3677
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD TSC1
[1] 155
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.27 0.376 1.67
strata=LOW 3 3 1.73 0.926 1.67
Chisq= 1.7 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.394 4.033 1.164 1.198 0.231
Likelihood ratio test=1.69 on 1 df, p=0.1937
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD BRD3
[1] 156
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 6.36 0.289 1.69
strata=LOW 3 3 1.64 1.118 1.69
Chisq= 1.7 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.137 3.116 0.920 1.235 0.217
Likelihood ratio test=1.56 on 1 df, p=0.2114
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD SLC16A1
[1] 157
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.23 0.0168 0.0449
strata=LOW 3 3 2.77 0.0197 0.0449
Chisq= 0 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1950 1.2153 0.9213 0.212 0.832
Likelihood ratio test=0.05 on 1 df, p=0.8315
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR132
============================
TCGA-COAD MIR375
============================
TCGA-COAD MIOX
[1] 158
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.8 0.133 4
strata=LOW 1 1 0.2 3.200 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.204e+01 3.739e+09 3.057e+04 0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD ATXN8OS
============================
TCGA-COAD KLHDC3
[1] 159
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.24 0.0173 0.0332
strata=LOW 5 5 4.76 0.0118 0.0332
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1410 1.1514 0.7745 0.182 0.856
Likelihood ratio test=0.03 on 1 df, p=0.8552
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD MICU1
[1] 160
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.68 0.0997 0.536
strata=LOW 2 2 1.32 0.3546 0.536
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.7222 2.0589 1.0075 0.717 0.474
Likelihood ratio test=0.5 on 1 df, p=0.478
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD CBS
[1] 161
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5 0.202 0.856
strata=LOW 3 3 2 0.506 0.856
Chisq= 0.9 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.8286 2.2902 0.9202 0.901 0.368
Likelihood ratio test=0.83 on 1 df, p=0.3615
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD HUWE1
[1] 162
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.67 0.0667 0.154
strata=LOW 2 2 2.33 0.0476 0.154
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.4812 0.6180 1.2380 -0.389 0.697
Likelihood ratio test=0.16 on 1 df, p=0.6913
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD LINC00472
[1] 163
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.75 0.902 1.41
strata=LOW 4 4 5.25 0.300 1.41
Chisq= 1.4 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.0483 0.3505 0.9216 -1.137 0.255
Likelihood ratio test=1.33 on 1 df, p=0.2494
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD FGF21
============================
TCGA-COAD MIR34A
============================
TCGA-COAD IDH1
[1] 164
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.82 0.237 0.594
strata=LOW 4 4 3.18 0.210 0.594
Chisq= 0.6 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.8475 2.3338 1.1303 0.75 0.453
Likelihood ratio test=0.65 on 1 df, p=0.4198
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD GSK3B
============================
TCGA-COAD KDM4A
[1] 165
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.77 0.156 0.825
strata=LOW 2 2 1.23 0.477 0.825
Chisq= 0.8 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.073 2.924 1.235 0.869 0.385
Likelihood ratio test=0.81 on 1 df, p=0.3677
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PEX12
[1] 166
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.12 0.699 0.985
strata=LOW 4 4 4.88 0.160 0.985
Chisq= 1 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.9671 0.3802 1.0107 -0.957 0.339
Likelihood ratio test=0.88 on 1 df, p=0.3471
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD IDO1
[1] 167
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 6.09 0.716 3.81
strata=LOW 4 4 1.91 2.281 3.81
Chisq= 3.8 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.925 6.855 1.131 1.702 0.0888
Likelihood ratio test=3.77 on 1 df, p=0.05213
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD BCAT2
[1] 168
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.52 0.509 2.56
strata=LOW 3 3 1.48 1.551 2.56
Chisq= 2.6 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.688 5.408 1.172 1.44 0.15
Likelihood ratio test=2.47 on 1 df, p=0.1159
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD ADAM23
[1] 169
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.41 1.786 2.82
strata=LOW 4 4 5.59 0.451 2.82
Chisq= 2.8 on 1 degrees of freedom, p= 0.09
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.7438 0.1748 1.1660 -1.496 0.135
Likelihood ratio test=2.68 on 1 df, p=0.1015
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD PEX3
[1] 170
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 1.08 0.00641 0.0105
strata=LOW 3 3 2.92 0.00238 0.0105
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1285 1.1372 1.2535 0.103 0.918
Likelihood ratio test=0.01 on 1 df, p=0.9178
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD ATP5MC3
[1] 171
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.85 0.01176 0.0191
strata=LOW 5 5 5.15 0.00423 0.0191
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1278 0.8801 0.9241 -0.138 0.89
Likelihood ratio test=0.02 on 1 df, p=0.8905
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD AQP5
[1] 172
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.48 0.0941 0.26
strata=LOW 3 3 2.52 0.0928 0.26
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.5892 1.8026 1.1718 0.503 0.615
Likelihood ratio test=0.27 on 1 df, p=0.6001
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD ADAMTS9-AS1
[1] 173
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.367 1.0939 1.34
strata=LOW 5 5 5.633 0.0712 1.34
Chisq= 1.3 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.4979 0.2236 1.4164 -1.058 0.29
Likelihood ratio test=1.03 on 1 df, p=0.3107
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD ACSL3
[1] 174
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.48 0.0941 0.26
strata=LOW 3 3 2.52 0.0928 0.26
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.5892 1.8026 1.1718 0.503 0.615
Likelihood ratio test=0.27 on 1 df, p=0.6001
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD DDR2
[1] 175
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.23 0.0168 0.0449
strata=LOW 3 3 2.77 0.0197 0.0449
Chisq= 0 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1950 1.2153 0.9213 0.212 0.832
Likelihood ratio test=0.05 on 1 df, p=0.8315
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD TERT
[1] 176
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.77 0.156 0.485
strata=LOW 3 3 2.23 0.263 0.485
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.6321 1.8815 0.9220 0.686 0.493
Likelihood ratio test=0.48 on 1 df, p=0.4874
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD IFNA7
============================
TCGA-COAD ECH1
[1] 177
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.95 0.000517 0.00159
strata=LOW 3 3 3.05 0.000672 0.00159
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.03534 0.96528 0.88617 -0.04 0.968
Likelihood ratio test=0 on 1 df, p=0.9681
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD CS
[1] 178
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.45 0.470 1.5
strata=LOW 4 4 2.55 0.818 1.5
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.046 2.845 0.888 1.178 0.239
Likelihood ratio test=1.49 on 1 df, p=0.2226
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD AMN
[1] 179
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.18 0.210 0.594
strata=LOW 2 2 2.82 0.237 0.594
Chisq= 0.6 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.8475 0.4285 1.1303 -0.75 0.453
Likelihood ratio test=0.65 on 1 df, p=0.4198
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD DUOX2
[1] 180
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 1.72 3.016 5.63
strata=LOW 3 3 5.28 0.984 5.63
Chisq= 5.6 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.172e+01 3.708e-10 2.077e+04 -0.001 0.999
Likelihood ratio test=7.11 on 1 df, p=0.007663
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MBOAT1
[1] 181
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.36 0.1234 0.219
strata=LOW 5 5 5.64 0.0734 0.219
Chisq= 0.2 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.3348 0.7155 0.7185 -0.466 0.641
Likelihood ratio test=0.22 on 1 df, p=0.6418
n= 9, number of events= 9
(15 observations deleted due to missingness)
============================
TCGA-COAD RNF113A
[1] 182
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.75 0.15 3
strata=LOW 1 1 0.25 2.25 3
Chisq= 3 on 1 degrees of freedom, p= 0.08
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.208e+01 3.903e+09 3.607e+04 0.001 1
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD MIR138-1
============================
TCGA-COAD MIR144
============================
TCGA-COAD P4HB
[1] 183
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.93 0.589 1.18
strata=LOW 2 2 3.07 0.371 1.18
Chisq= 1.2 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.2084 0.2987 1.1730 -1.03 0.303
Likelihood ratio test=1.23 on 1 df, p=0.2675
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MIR338
============================
TCGA-COAD PTGS2
[1] 184
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.55 0.818 1.5
strata=LOW 4 4 5.45 0.384 1.5
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.0456 0.3515 0.8880 -1.178 0.239
Likelihood ratio test=1.49 on 1 df, p=0.2226
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD ASAH2
[1] 185
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.33 0.333 0.615
strata=LOW 2 2 2.67 0.167 0.615
Chisq= 0.6 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.9406 0.3904 1.2403 -0.758 0.448
Likelihood ratio test=0.62 on 1 df, p=0.4325
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD MIR522
============================
TCGA-COAD GALNT14
[1] 186
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.05 0.000495 0.00353
strata=LOW 1 1 0.95 0.002632 0.00353
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.06936 1.07182 1.16790 0.059 0.953
Likelihood ratio test=0 on 1 df, p=0.9529
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD KDM4C
[1] 187
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.32 0.3546 0.536
strata=LOW 4 4 4.68 0.0997 0.536
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7222 0.4857 1.0075 -0.717 0.474
Likelihood ratio test=0.5 on 1 df, p=0.478
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD FXN
[1] 188
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.33 0.0476 0.154
strata=LOW 2 2 1.67 0.0667 0.154
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4812 1.6180 1.2380 0.389 0.697
Likelihood ratio test=0.16 on 1 df, p=0.6913
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD MEF2C
[1] 189
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.41 1.786 2.82
strata=LOW 4 4 5.59 0.451 2.82
Chisq= 2.8 on 1 degrees of freedom, p= 0.09
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.7438 0.1748 1.1660 -1.496 0.135
Likelihood ratio test=2.68 on 1 df, p=0.1015
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MDM2
[1] 190
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.98 9.31e-05 0.000242
strata=LOW 3 3 3.02 9.21e-05 0.000242
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.01448 0.98563 0.93137 -0.016 0.988
Likelihood ratio test=0 on 1 df, p=0.9876
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MAP3K14
[1] 191
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.633 0.0712 1.34
strata=LOW 1 1 0.367 1.0939 1.34
Chisq= 1.3 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.498 4.472 1.416 1.058 0.29
Likelihood ratio test=1.03 on 1 df, p=0.3107
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MDM4
[1] 192
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.4 0.2547 0.359
strata=LOW 5 5 5.6 0.0638 0.359
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5445 0.5801 0.9202 -0.592 0.554
Likelihood ratio test=0.33 on 1 df, p=0.5629
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD ASMTL-AS1
[1] 193
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.93 0.589 1.18
strata=LOW 3 3 4.07 0.280 1.18
Chisq= 1.2 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.2084 0.2987 1.1730 -1.03 0.303
Likelihood ratio test=1.23 on 1 df, p=0.2675
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD NEAT1
[1] 194
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.833 1.63 2.88
strata=LOW 2 2 3.167 0.43 2.88
Chisq= 2.9 on 1 degrees of freedom, p= 0.09
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.168e+01 3.848e-10 2.943e+04 -0.001 0.999
Likelihood ratio test=3.58 on 1 df, p=0.05836
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD COPZ1
[1] 195
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.23 0.263 0.485
strata=LOW 3 3 3.77 0.156 0.485
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.6321 0.5315 0.9220 -0.686 0.493
Likelihood ratio test=0.48 on 1 df, p=0.4874
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PLIN2
[1] 196
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.75 0.0160 0.044
strata=LOW 3 3 3.25 0.0185 0.044
Chisq= 0 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1838 0.8321 0.8774 -0.209 0.834
Likelihood ratio test=0.04 on 1 df, p=0.8326
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD FADS2
[1] 197
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.32 0.3546 0.536
strata=LOW 4 4 4.68 0.0997 0.536
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7222 0.4857 1.0075 -0.717 0.474
Likelihood ratio test=0.5 on 1 df, p=0.478
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR7-1
============================
TCGA-COAD TXN
[1] 198
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.45 0.388 2.04
strata=LOW 3 3 1.55 1.370 2.04
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.2510 3.4940 0.9283 1.348 0.178
Likelihood ratio test=1.85 on 1 df, p=0.1734
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR302A
============================
TCGA-COAD EGLN2
[1] 199
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.83 0.01039 0.0206
strata=LOW 4 4 4.17 0.00705 0.0206
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1196 0.8872 0.8348 -0.143 0.886
Likelihood ratio test=0.02 on 1 df, p=0.8861
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD NCOA3
[1] 200
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.23 0.0168 0.0449
strata=LOW 3 3 2.77 0.0197 0.0449
Chisq= 0 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1950 1.2153 0.9213 0.212 0.832
Likelihood ratio test=0.05 on 1 df, p=0.8315
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD SREBF1
[1] 201
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.92 0.00238 0.0105
strata=LOW 1 1 1.08 0.00641 0.0105
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1285 0.8794 1.2535 -0.103 0.918
Likelihood ratio test=0.01 on 1 df, p=0.9178
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD LINC01134
[1] 202
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.43 0.132 0.265
strata=LOW 3 3 3.57 0.090 0.265
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.4730 0.6231 0.9269 -0.51 0.61
Likelihood ratio test=0.27 on 1 df, p=0.6059
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MYCN
[1] 203
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.48 0.0941 0.26
strata=LOW 3 3 2.52 0.0928 0.26
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.5892 1.8026 1.1718 0.503 0.615
Likelihood ratio test=0.27 on 1 df, p=0.6001
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD IFNA4
============================
TCGA-COAD DPEP1
[1] 204
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.23 0.477 0.825
strata=LOW 3 3 3.77 0.156 0.825
Chisq= 0.8 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.073 0.342 1.235 -0.869 0.385
Likelihood ratio test=0.81 on 1 df, p=0.3677
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD VDAC2
[1] 205
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.783 0.0599 0.0824
strata=LOW 4 4 4.217 0.0111 0.0824
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.3530 0.7026 1.2359 -0.286 0.775
Likelihood ratio test=0.08 on 1 df, p=0.7797
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PCBP2-OT1
[1] 206
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.4 0.0667 0.135
strata=LOW 4 4 3.6 0.0444 0.135
Chisq= 0.1 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.3429 1.4090 0.9368 0.366 0.714
Likelihood ratio test=0.14 on 1 df, p=0.712
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD KEAP1
[1] 207
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.85 0.706 5.05
strata=LOW 3 3 1.15 2.976 5.05
Chisq= 5.1 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.194e+01 3.381e+09 2.480e+04 0.001 0.999
Likelihood ratio test=5.99 on 1 df, p=0.01438
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD RPL8
[1] 208
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.95 0.000517 0.00159
strata=LOW 3 3 3.05 0.000672 0.00159
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.03534 0.96528 0.88617 -0.04 0.968
Likelihood ratio test=0 on 1 df, p=0.9681
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD ALOX12
============================
TCGA-COAD ACSF2
[1] 209
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.167 0.43 2.88
strata=LOW 2 2 0.833 1.63 2.88
Chisq= 2.9 on 1 degrees of freedom, p= 0.09
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.168e+01 2.599e+09 2.943e+04 0.001 0.999
Likelihood ratio test=3.58 on 1 df, p=0.05836
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD KDM5A
[1] 210
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 2.08 0.563 1.78
strata=LOW 3 3 1.92 0.612 1.78
Chisq= 1.8 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.085e+01 1.136e+09 2.490e+04 0.001 0.999
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD NRAS
[1] 211
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.783 0.0599 0.0824
strata=LOW 4 4 4.217 0.0111 0.0824
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.3530 0.7026 1.2359 -0.286 0.775
Likelihood ratio test=0.08 on 1 df, p=0.7797
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MIR30E
============================
TCGA-COAD OGFRP1
[1] 212
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.87 0.196 0.455
strata=LOW 5 5 4.13 0.183 0.455
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.5617 1.7536 0.8430 0.666 0.505
Likelihood ratio test=0.48 on 1 df, p=0.4906
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD TF
[1] 213
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.72 0.0163 0.052
strata=LOW 3 3 3.28 0.0235 0.052
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1938 0.8238 0.8515 -0.228 0.82
Likelihood ratio test=0.05 on 1 df, p=0.8177
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD ETV4
[1] 214
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 1.83 0.379 1.47
strata=LOW 2 2 1.17 0.595 1.47
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.097e+01 1.286e+09 2.928e+04 0.001 0.999
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD PLA2G6
[1] 215
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.27 0.237 0.559
strata=LOW 2 2 2.73 0.197 0.559
Chisq= 0.6 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.8455 0.4293 1.1634 -0.727 0.467
Likelihood ratio test=0.59 on 1 df, p=0.4413
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD POR
[1] 216
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.667 0.167 2
strata=LOW 1 1 0.333 1.333 2
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.215e+01 4.171e+09 4.566e+04 0 1
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD BRPF1
[1] 217
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 6.038 0.688 6.62
strata=LOW 3 3 0.962 4.318 6.62
Chisq= 6.6 on 1 degrees of freedom, p= 0.01
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.242e+01 5.456e+09 2.728e+04 0.001 0.999
Likelihood ratio test=7.11 on 1 df, p=0.007663
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD TMBIM4
[1] 218
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 2.45 0.858 2.19
strata=LOW 5 5 3.55 0.592 2.19
Chisq= 2.2 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.071e+01 9.910e+08 2.083e+04 0.001 0.999
Likelihood ratio test=3.58 on 1 df, p=0.05836
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD KRAS
[1] 219
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.62 0.145 0.365
strata=LOW 4 4 3.38 0.112 0.365
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.6766 1.9672 1.1392 0.594 0.553
Likelihood ratio test=0.4 on 1 df, p=0.529
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD AHCY
[1] 220
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.57 0.1199 0.201
strata=LOW 4 4 4.43 0.0424 0.201
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.4492 0.6381 1.0100 -0.445 0.657
Likelihood ratio test=0.2 on 1 df, p=0.6578
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR34C
============================
TCGA-COAD ATG3
[1] 221
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.36 0.1724 0.337
strata=LOW 4 4 4.64 0.0878 0.337
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5328 0.5870 0.9273 -0.575 0.566
Likelihood ratio test=0.34 on 1 df, p=0.5611
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR30B
============================
TCGA-COAD LYRM1
[1] 222
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.9 0.281 0.654
strata=LOW 5 5 4.1 0.199 0.654
Chisq= 0.7 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.8731 2.3943 1.1117 0.785 0.432
Likelihood ratio test=0.73 on 1 df, p=0.3923
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD SIRT6
[1] 223
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.67 0.0667 0.154
strata=LOW 2 2 2.33 0.0476 0.154
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.4812 0.6180 1.2380 -0.389 0.697
Likelihood ratio test=0.16 on 1 df, p=0.6913
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD KMT2D
[1] 224
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.14 0.237 0.51
strata=LOW 3 3 3.86 0.192 0.51
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.6164 0.5399 0.8761 -0.704 0.482
Likelihood ratio test=0.52 on 1 df, p=0.4702
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD LPIN1
[1] 225
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.48 0.0941 0.26
strata=LOW 3 3 2.52 0.0928 0.26
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.5892 1.8026 1.1718 0.503 0.615
Likelihood ratio test=0.27 on 1 df, p=0.6001
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MBOAT2
[1] 226
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.77 0.156 0.825
strata=LOW 2 2 1.23 0.477 0.825
Chisq= 0.8 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.073 2.924 1.235 0.869 0.385
Likelihood ratio test=0.81 on 1 df, p=0.3677
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD KDM3B
[1] 227
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.5 0.497 1.85
strata=LOW 4 4 2.5 0.893 1.85
Chisq= 1.9 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.430 4.177 1.133 1.261 0.207
Likelihood ratio test=1.98 on 1 df, p=0.159
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD ARHGEF26-AS1
[1] 228
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.2 3.200 4
strata=LOW 4 4 4.8 0.133 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.204e+01 2.674e-10 3.057e+04 -0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(20 observations deleted due to missingness)
============================
TCGA-COAD MIR9-1
============================
TCGA-COAD AIFM2
[1] 229
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.52 0.0928 0.26
strata=LOW 2 2 2.48 0.0941 0.26
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5892 0.5548 1.1718 -0.503 0.615
Likelihood ratio test=0.27 on 1 df, p=0.6001
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PRDX1
[1] 230
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.45 0.388 2.04
strata=LOW 3 3 1.55 1.370 2.04
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.2510 3.4940 0.9283 1.348 0.178
Likelihood ratio test=1.85 on 1 df, p=0.1734
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD FOXO4
[1] 231
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.35 0.419 4.26
strata=LOW 2 2 0.65 2.804 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.232e+01 4.923e+09 3.308e+04 0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD BMAL1
[1] 232
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.82 0.01850 0.03
strata=LOW 4 4 4.18 0.00803 0.03
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1603 0.8519 0.9273 -0.173 0.863
Likelihood ratio test=0.03 on 1 df, p=0.8635
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR127
============================
TCGA-COAD TGFBR1
[1] 233
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.92 0.612 1.78
strata=LOW 1 1 2.08 0.563 1.78
Chisq= 1.8 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.085e+01 8.800e-10 2.490e+04 -0.001 0.999
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD NR1D2
[1] 234
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.33 0.0476 0.154
strata=LOW 2 2 1.67 0.0667 0.154
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4812 1.6180 1.2380 0.389 0.697
Likelihood ratio test=0.16 on 1 df, p=0.6913
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD FZD7
[1] 235
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.92 0.612 1.78
strata=LOW 1 1 2.08 0.563 1.78
Chisq= 1.8 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.085e+01 8.800e-10 2.490e+04 -0.001 0.999
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD G6PD
[1] 236
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.75 0.15 3
strata=LOW 1 1 0.25 2.25 3
Chisq= 3 on 1 degrees of freedom, p= 0.08
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.208e+01 3.903e+09 3.607e+04 0.001 1
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD HRAS
[1] 237
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.8 0.133 4
strata=LOW 1 1 0.2 3.200 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.204e+01 3.739e+09 3.057e+04 0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD SLC38A1
[1] 238
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.48 0.1800 0.297
strata=LOW 3 3 3.52 0.0759 0.297
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5493 0.5774 1.0198 -0.539 0.59
Likelihood ratio test=0.29 on 1 df, p=0.5922
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD SLC39A14
[1] 239
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.52 0.509 2.56
strata=LOW 3 3 1.48 1.551 2.56
Chisq= 2.6 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.688 5.408 1.172 1.44 0.15
Likelihood ratio test=2.47 on 1 df, p=0.1159
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR21
============================
TCGA-COAD MIR1-1
============================
TCGA-COAD PROM2
[1] 240
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.62 0.0909 0.141
strata=LOW 4 4 4.38 0.0335 0.141
Chisq= 0.1 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.3503 0.7045 0.9368 -0.374 0.708
Likelihood ratio test=0.14 on 1 df, p=0.712
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD NFE2L2
[1] 241
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.48 0.0941 0.26
strata=LOW 3 3 2.52 0.0928 0.26
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.5892 1.8026 1.1718 0.503 0.615
Likelihood ratio test=0.27 on 1 df, p=0.6001
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD GABARAPL1
[1] 242
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 3.31 0.857 2.05
strata=LOW 2 2 3.69 0.771 2.05
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.4814 0.2273 1.1187 -1.324 0.185
Likelihood ratio test=2.27 on 1 df, p=0.1317
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR335
============================
TCGA-COAD PTEN
[1] 243
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PARP4
[1] 244
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.983 1.051 1.59
strata=LOW 3 3 4.017 0.257 1.59
Chisq= 1.6 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.4388 0.2372 1.2359 -1.164 0.244
Likelihood ratio test=1.46 on 1 df, p=0.2262
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MS4A15
[1] 245
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.27 0.4210 0.626
strata=LOW 5 5 5.73 0.0932 0.626
Chisq= 0.6 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7787 0.4590 1.0083 -0.772 0.44
Likelihood ratio test=0.58 on 1 df, p=0.4453
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD TIMM9
[1] 246
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.48 0.1800 0.297
strata=LOW 3 3 3.52 0.0759 0.297
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5493 0.5774 1.0198 -0.539 0.59
Likelihood ratio test=0.29 on 1 df, p=0.5922
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PARP3
[1] 247
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.77 0.156 0.825
strata=LOW 2 2 1.23 0.477 0.825
Chisq= 0.8 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.073 2.924 1.235 0.869 0.385
Likelihood ratio test=0.81 on 1 df, p=0.3677
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD WIPI1
[1] 248
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 3.76 0.407 0.904
strata=LOW 3 3 4.24 0.361 0.904
Chisq= 0.9 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7860 0.4557 0.8464 -0.929 0.353
Likelihood ratio test=0.94 on 1 df, p=0.3319
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD SNX5
[1] 249
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.77 0.156 0.485
strata=LOW 3 3 2.23 0.263 0.485
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.6321 1.8815 0.9220 0.686 0.493
Likelihood ratio test=0.48 on 1 df, p=0.4874
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD LINC00239
[1] 250
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.77 0.156 0.485
strata=LOW 3 3 2.23 0.263 0.485
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.6321 1.8815 0.9220 0.686 0.493
Likelihood ratio test=0.48 on 1 df, p=0.4874
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PIEZO1
[1] 251
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.333 1.333 2
strata=LOW 2 2 2.667 0.167 2
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.215e+01 2.398e-10 4.566e+04 0 1
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD AKR1C2
[1] 252
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.41 0.1434 0.248
strata=LOW 4 4 4.59 0.0754 0.248
Chisq= 0.2 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.4115 0.6627 0.8315 -0.495 0.621
Likelihood ratio test=0.24 on 1 df, p=0.6217
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR4443
============================
TCGA-COAD SLC16A1-AS1
[1] 253
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.2 3.200 4
strata=LOW 4 4 4.8 0.133 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.204e+01 2.674e-10 3.057e+04 -0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD FAR1
============================
TCGA-COAD CISD2
[1] 254
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.27 0.0218 0.0739
strata=LOW 2 2 1.73 0.0410 0.0739
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.2739 1.3151 1.0107 0.271 0.786
Likelihood ratio test=0.07 on 1 df, p=0.7866
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MAPK3
[1] 255
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3 0.330 0.68
strata=LOW 3 3 4 0.248 0.68
Chisq= 0.7 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7106 0.4913 0.8786 -0.809 0.419
Likelihood ratio test=0.69 on 1 df, p=0.405
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD CYGB
[1] 256
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.5 0.0729 0.149
strata=LOW 4 4 4.5 0.0566 0.149
Chisq= 0.1 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.2975 0.7427 0.7727 -0.385 0.7
Likelihood ratio test=0.15 on 1 df, p=0.6988
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD MLST8
[1] 257
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.85 0.706 5.05
strata=LOW 3 3 1.15 2.976 5.05
Chisq= 5.1 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.194e+01 3.381e+09 2.480e+04 0.001 0.999
Likelihood ratio test=5.99 on 1 df, p=0.01438
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PANX2
[1] 258
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 6.348 0.286 3.61
strata=LOW 2 2 0.652 2.784 3.61
Chisq= 3.6 on 1 degrees of freedom, p= 0.06
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.012 7.475 1.236 1.628 0.104
Likelihood ratio test=2.83 on 1 df, p=0.09274
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD PEBP1
[1] 259
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 6.181 0.226 2.38
strata=LOW 2 2 0.819 1.703 2.38
Chisq= 2.4 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.705 5.502 1.236 1.379 0.168
Likelihood ratio test=2.05 on 1 df, p=0.1523
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD PARP8
[1] 260
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.45 0.6722 0.871
strata=LOW 4 4 4.55 0.0665 0.871
Chisq= 0.9 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.2425 0.2887 1.4179 -0.876 0.381
Likelihood ratio test=0.72 on 1 df, p=0.395
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD GJA1
[1] 261
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 3.8 0.382 0.871
strata=LOW 3 3 4.2 0.345 0.871
Chisq= 0.9 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7793 0.4587 0.8539 -0.913 0.361
Likelihood ratio test=0.91 on 1 df, p=0.3407
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD BAP1
[1] 262
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.24 0.0173 0.0332
strata=LOW 5 5 4.76 0.0118 0.0332
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1410 1.1514 0.7745 0.182 0.856
Likelihood ratio test=0.03 on 1 df, p=0.8552
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD MAP3K11
[1] 263
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.92 0.00238 0.0105
strata=LOW 1 1 1.08 0.00641 0.0105
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1285 0.8794 1.2535 -0.103 0.918
Likelihood ratio test=0.01 on 1 df, p=0.9178
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD TTBK2
[1] 264
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.14 0.237 0.51
strata=LOW 3 3 3.86 0.192 0.51
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.6164 0.5399 0.8761 -0.704 0.482
Likelihood ratio test=0.52 on 1 df, p=0.4702
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR214
============================
TCGA-COAD PARP15
[1] 265
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.16 0.00630 0.0154
strata=LOW 4 4 3.84 0.00683 0.0154
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.09533 1.10002 0.76955 0.124 0.901
Likelihood ratio test=0.02 on 1 df, p=0.9012
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD HDDC3
[1] 266
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.67 0.0965 0.268
strata=LOW 4 4 3.33 0.1354 0.268
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4006 1.4928 0.7779 0.515 0.607
Likelihood ratio test=0.27 on 1 df, p=0.6045
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR10A
============================
TCGA-COAD CGAS
[1] 267
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.66 0.673 1.23
strata=LOW 4 4 5.34 0.335 1.23
Chisq= 1.2 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.9348 0.3927 0.8729 -1.071 0.284
Likelihood ratio test=1.23 on 1 df, p=0.2675
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD SIRT2
[1] 268
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.52 0.0928 0.26
strata=LOW 2 2 2.48 0.0941 0.26
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5892 0.5548 1.1718 -0.503 0.615
Likelihood ratio test=0.27 on 1 df, p=0.6001
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PPARD
[1] 269
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.15 2.976 5.05
strata=LOW 3 3 4.85 0.706 5.05
Chisq= 5.1 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.194e+01 2.957e-10 2.480e+04 -0.001 0.999
Likelihood ratio test=5.99 on 1 df, p=0.01438
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD EGR1
[1] 270
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.41 1.046 1.81
strata=LOW 4 4 5.59 0.451 1.81
Chisq= 1.8 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.1303 0.3229 0.8813 -1.283 0.2
Likelihood ratio test=1.77 on 1 df, p=0.1832
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD AQP3
[1] 271
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.5 0.497 1.85
strata=LOW 4 4 2.5 0.893 1.85
Chisq= 1.9 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.430 4.177 1.133 1.261 0.207
Likelihood ratio test=1.98 on 1 df, p=0.159
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD HSF1
[1] 272
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.75 0.15 3
strata=LOW 1 1 0.25 2.25 3
Chisq= 3 on 1 degrees of freedom, p= 0.08
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.208e+01 3.903e+09 3.607e+04 0.001 1
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD MIR18A
============================
TCGA-COAD OSBPL9
[1] 273
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.833 1.63 2.88
strata=LOW 2 2 3.167 0.43 2.88
Chisq= 2.9 on 1 degrees of freedom, p= 0.09
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.168e+01 3.848e-10 2.943e+04 -0.001 0.999
Likelihood ratio test=3.58 on 1 df, p=0.05836
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD SESN2
[1] 274
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.18 0.210 0.594
strata=LOW 2 2 2.82 0.237 0.594
Chisq= 0.6 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.8475 0.4285 1.1303 -0.75 0.453
Likelihood ratio test=0.65 on 1 df, p=0.4198
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD BECN1
[1] 275
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.45 0.0464 0.135
strata=LOW 4 4 3.55 0.0583 0.135
Chisq= 0.1 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.2873 1.3329 0.7856 0.366 0.715
Likelihood ratio test=0.13 on 1 df, p=0.7165
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD FTMT
============================
TCGA-COAD HCAR1
[1] 276
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.64 1.118 1.69
strata=LOW 5 5 6.36 0.289 1.69
Chisq= 1.7 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.1366 0.3209 0.9200 -1.235 0.217
Likelihood ratio test=1.56 on 1 df, p=0.2114
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD HILPDA
[1] 277
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=10, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.01 1.01e-05 1.84e-05
strata=LOW 6 6 5.99 6.73e-06 1.84e-05
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.002894 1.002898 0.675220 0.004 0.997
Likelihood ratio test=0 on 1 df, p=0.9966
n= 10, number of events= 10
(14 observations deleted due to missingness)
============================
TCGA-COAD GSTM1
[1] 278
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3 0.330 0.68
strata=LOW 3 3 4 0.248 0.68
Chisq= 0.7 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7106 0.4913 0.8786 -0.809 0.419
Likelihood ratio test=0.69 on 1 df, p=0.405
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR222
============================
TCGA-COAD RARRES2
[1] 279
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3 0.330 0.68
strata=LOW 3 3 4 0.248 0.68
Chisq= 0.7 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7106 0.4913 0.8786 -0.809 0.419
Likelihood ratio test=0.69 on 1 df, p=0.405
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD BRD4
[1] 280
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.667 0.167 2
strata=LOW 1 1 0.333 1.333 2
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.215e+01 4.171e+09 4.566e+04 0 1
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD SOCS1
[1] 281
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.8 0.133 4
strata=LOW 1 1 0.2 3.200 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.204e+01 3.739e+09 3.057e+04 0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MIR17
============================
TCGA-COAD GDF15
[1] 282
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.17 0.216 0.48
strata=LOW 3 3 3.83 0.179 0.48
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.6053 0.5459 0.8851 -0.684 0.494
Likelihood ratio test=0.49 on 1 df, p=0.483
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD ARF6
[1] 283
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.98 9.31e-05 0.000242
strata=LOW 3 3 3.02 9.21e-05 0.000242
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.01448 0.98563 0.93137 -0.016 0.988
Likelihood ratio test=0 on 1 df, p=0.9876
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD CDO1
[1] 284
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.93 0.146 1.12
strata=LOW 2 2 1.07 0.811 1.12
Chisq= 1.1 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.023 2.783 1.008 1.015 0.31
Likelihood ratio test=0.99 on 1 df, p=0.3196
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD CAMKK2
[1] 285
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.73 0.0410 0.0739
strata=LOW 3 3 3.27 0.0218 0.0739
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.2739 0.7604 1.0107 -0.271 0.786
Likelihood ratio test=0.07 on 1 df, p=0.7866
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD LINC01606
[1] 286
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=11, 31 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.37 1.113 1.63
strata=LOW 7 7 8.63 0.306 1.63
Chisq= 1.6 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.8948 0.4087 0.7216 -1.24 0.215
Likelihood ratio test=1.5 on 1 df, p=0.2213
n= 11, number of events= 11
(31 observations deleted due to missingness)
============================
TCGA-COAD BACH1
[1] 287
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.9 0.926 3.86
strata=LOW 4 4 2.1 1.719 3.86
Chisq= 3.9 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.129e+01 1.754e+09 2.052e+04 0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD DPP4
[1] 288
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=10, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.05 0.000511 0.00119
strata=LOW 5 5 4.95 0.000521 0.00119
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.02337 1.02364 0.67865 0.034 0.973
Likelihood ratio test=0 on 1 df, p=0.9725
n= 10, number of events= 10
(14 observations deleted due to missingness)
============================
TCGA-COAD PPP1R13L
[1] 289
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 6.66 0.0649 0.424
strata=LOW 2 2 1.34 0.3216 0.424
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.5651 1.7596 0.8787 0.643 0.52
Likelihood ratio test=0.39 on 1 df, p=0.5343
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR150
============================
TCGA-COAD FLT3
[1] 290
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.41 1.046 1.81
strata=LOW 4 4 5.59 0.451 1.81
Chisq= 1.8 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.1303 0.3229 0.8813 -1.283 0.2
Likelihood ratio test=1.77 on 1 df, p=0.1832
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD MAP1LC3A
[1] 291
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.26 0.127 0.466
strata=LOW 2 2 2.74 0.198 0.466
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7485 0.4731 1.1196 -0.668 0.504
Likelihood ratio test=0.52 on 1 df, p=0.4724
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD A2M-AS1
[1] 292
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.23 0.0168 0.0449
strata=LOW 3 3 2.77 0.0197 0.0449
Chisq= 0 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1950 1.2153 0.9213 0.212 0.832
Likelihood ratio test=0.05 on 1 df, p=0.8315
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PDSS2
[1] 293
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.15 0.01079 0.0162
strata=LOW 6 6 5.85 0.00397 0.0162
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1085 1.1146 0.8527 0.127 0.899
Likelihood ratio test=0.02 on 1 df, p=0.8981
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD DNAJB6
[1] 294
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.2 0.0119 0.0262
strata=LOW 4 4 3.8 0.0100 0.0262
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1336 1.1430 0.8268 0.162 0.872
Likelihood ratio test=0.03 on 1 df, p=0.8716
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD SUV39H1
[1] 295
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.167 0.43 2.88
strata=LOW 2 2 0.833 1.63 2.88
Chisq= 2.9 on 1 degrees of freedom, p= 0.09
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.168e+01 2.599e+09 2.943e+04 0.001 0.999
Likelihood ratio test=3.58 on 1 df, p=0.05836
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD LPCAT3
[1] 296
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.33 0.333 0.615
strata=LOW 2 2 2.67 0.167 0.615
Chisq= 0.6 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.9406 0.3904 1.2403 -0.758 0.448
Likelihood ratio test=0.62 on 1 df, p=0.4325
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD MIR761
============================
TCGA-COAD CDCA3
[1] 297
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.667 0.167 2
strata=LOW 1 1 0.333 1.333 2
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.215e+01 4.171e+09 4.566e+04 0 1
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD EPAS1
[1] 298
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.6 0.0444 0.135
strata=LOW 2 2 2.4 0.0667 0.135
Chisq= 0.1 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.3429 0.7097 0.9368 -0.366 0.714
Likelihood ratio test=0.14 on 1 df, p=0.712
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD SLC11A2
[1] 299
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 1.08 0.00641 0.0105
strata=LOW 3 3 2.92 0.00238 0.0105
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1285 1.1372 1.2535 0.103 0.918
Likelihood ratio test=0.01 on 1 df, p=0.9178
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD CREB3
[1] 300
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.833 1.63 2.88
strata=LOW 2 2 3.167 0.43 2.88
Chisq= 2.9 on 1 degrees of freedom, p= 0.09
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.168e+01 3.848e-10 2.943e+04 -0.001 0.999
Likelihood ratio test=3.58 on 1 df, p=0.05836
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD ATF3
[1] 301
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.55 0.818 1.5
strata=LOW 3 3 4.45 0.470 1.5
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.0456 0.3515 0.8880 -1.178 0.239
Likelihood ratio test=1.49 on 1 df, p=0.2226
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD TGFB1
[1] 302
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.017 0.257 1.59
strata=LOW 2 2 0.983 1.051 1.59
Chisq= 1.6 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.439 4.215 1.236 1.164 0.244
Likelihood ratio test=1.46 on 1 df, p=0.2262
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD SMG9
[1] 303
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.467 0.393 5.63
strata=LOW 2 2 0.533 4.033 5.63
Chisq= 5.6 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.195e+01 3.399e+09 2.380e+04 0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD NOX4
[1] 304
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.1 0.00187 0.00765
strata=LOW 2 2 1.9 0.00501 0.00765
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.07734 1.08041 0.88462 0.087 0.93
Likelihood ratio test=0.01 on 1 df, p=0.9306
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR27A
============================
TCGA-COAD FOXP1
[1] 305
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.33 0.0476 0.154
strata=LOW 2 2 1.67 0.0667 0.154
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4812 1.6180 1.2380 0.389 0.697
Likelihood ratio test=0.16 on 1 df, p=0.6913
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD SNCA
============================
TCGA-COAD ENPP2
[1] 306
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.05 1.868 2.97
strata=LOW 4 4 5.95 0.642 2.97
Chisq= 3 on 1 degrees of freedom, p= 0.08
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.4216 0.2413 0.8862 -1.604 0.109
Likelihood ratio test=2.77 on 1 df, p=0.0958
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD BRD2
[1] 307
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.33 0.0476 0.154
strata=LOW 2 2 1.67 0.0667 0.154
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4812 1.6180 1.2380 0.389 0.697
Likelihood ratio test=0.16 on 1 df, p=0.6913
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD ISCU
[1] 308
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.27 0.0218 0.0739
strata=LOW 2 2 1.73 0.0410 0.0739
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.2739 1.3151 1.0107 0.271 0.786
Likelihood ratio test=0.07 on 1 df, p=0.7866
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PHF21A
[1] 309
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.05 0.000495 0.00353
strata=LOW 1 1 0.95 0.002632 0.00353
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.06936 1.07182 1.16790 0.059 0.953
Likelihood ratio test=0 on 1 df, p=0.9529
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PARP6
[1] 310
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.17 0.595 1.47
strata=LOW 1 1 1.83 0.379 1.47
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.097e+01 7.775e-10 2.928e+04 -0.001 0.999
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD ZEB1
[1] 311
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.25 0.254 0.417
strata=LOW 4 4 4.75 0.120 0.417
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5293 0.5890 0.8287 -0.639 0.523
Likelihood ratio test=0.4 on 1 df, p=0.5252
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD LIG3
[1] 312
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.48 0.1800 0.297
strata=LOW 3 3 3.52 0.0759 0.297
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5493 0.5774 1.0198 -0.539 0.59
Likelihood ratio test=0.29 on 1 df, p=0.5922
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PEDS1
[1] 313
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.27 0.237 0.559
strata=LOW 2 2 2.73 0.197 0.559
Chisq= 0.6 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.8455 0.4293 1.1634 -0.727 0.467
Likelihood ratio test=0.59 on 1 df, p=0.4413
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD RPPH1
============================
TCGA-COAD GFRA1
[1] 314
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.9 0.00501 0.00765
strata=LOW 5 5 5.1 0.00187 0.00765
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.07734 0.92557 0.88462 -0.087 0.93
Likelihood ratio test=0.01 on 1 df, p=0.9306
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD AQP8
[1] 315
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.45 0.6722 0.871
strata=LOW 4 4 4.55 0.0665 0.871
Chisq= 0.9 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.2425 0.2887 1.4179 -0.876 0.381
Likelihood ratio test=0.72 on 1 df, p=0.395
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD SIRT1
[1] 316
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.48 0.0941 0.26
strata=LOW 3 3 2.52 0.0928 0.26
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.5892 1.8026 1.1718 0.503 0.615
Likelihood ratio test=0.27 on 1 df, p=0.6001
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MIR15A
============================
TCGA-COAD AKR1C3
[1] 317
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.41 0.1434 0.248
strata=LOW 4 4 4.59 0.0754 0.248
Chisq= 0.2 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.4115 0.6627 0.8315 -0.495 0.621
Likelihood ratio test=0.24 on 1 df, p=0.6217
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD DLD
[1] 318
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.32 0.3546 0.536
strata=LOW 4 4 4.68 0.0997 0.536
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7222 0.4857 1.0075 -0.717 0.474
Likelihood ratio test=0.5 on 1 df, p=0.478
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD USP11
[1] 319
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.92 0.612 1.78
strata=LOW 1 1 2.08 0.563 1.78
Chisq= 1.8 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.085e+01 8.800e-10 2.490e+04 -0.001 0.999
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD SREBF2
[1] 320
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 1.72 3.016 5.63
strata=LOW 3 3 5.28 0.984 5.63
Chisq= 5.6 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.172e+01 3.708e-10 2.077e+04 -0.001 0.999
Likelihood ratio test=7.11 on 1 df, p=0.007663
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR190A
============================
TCGA-COAD IFNA8
============================
TCGA-COAD KDM6B
[1] 321
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.55 0.0665 0.871
strata=LOW 1 1 0.45 0.6722 0.871
Chisq= 0.9 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.242 3.464 1.418 0.876 0.381
Likelihood ratio test=0.72 on 1 df, p=0.395
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD ACOT1
[1] 322
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.85 0.706 5.05
strata=LOW 3 3 1.15 2.976 5.05
Chisq= 5.1 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.194e+01 3.381e+09 2.480e+04 0.001 0.999
Likelihood ratio test=5.99 on 1 df, p=0.01438
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD RELA
============================
TCGA-COAD SLC39A7
[1] 323
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.33 0.0476 0.154
strata=LOW 2 2 1.67 0.0667 0.154
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4812 1.6180 1.2380 0.389 0.697
Likelihood ratio test=0.16 on 1 df, p=0.6913
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD POM121L12
============================
TCGA-COAD MIR101-1
============================
TCGA-COAD GABPB1-AS1
[1] 324
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.24 0.473 0.64
strata=LOW 5 5 5.76 0.101 0.64
Chisq= 0.6 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7244 0.4846 0.9243 -0.784 0.433
Likelihood ratio test=0.58 on 1 df, p=0.4477
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD EGFR
[1] 325
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 1.08 0.00641 0.0105
strata=LOW 3 3 2.92 0.00238 0.0105
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1285 1.1372 1.2535 0.103 0.918
Likelihood ratio test=0.01 on 1 df, p=0.9178
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD BRD7
[1] 326
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.61 1.198 1.68
strata=LOW 5 5 6.39 0.302 1.68
Chisq= 1.7 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.0351 0.3552 0.8310 -1.246 0.213
Likelihood ratio test=1.49 on 1 df, p=0.2217
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR1287
============================
TCGA-COAD MIR23A
============================
TCGA-COAD LCE2C
============================
TCGA-COAD ADAMTS13
[1] 327
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3 0.330 0.68
strata=LOW 3 3 4 0.248 0.68
Chisq= 0.7 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7106 0.4913 0.8786 -0.809 0.419
Likelihood ratio test=0.69 on 1 df, p=0.405
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD SIRT3
[1] 328
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.27 0.237 0.559
strata=LOW 2 2 2.73 0.197 0.559
Chisq= 0.6 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.8455 0.4293 1.1634 -0.727 0.467
Likelihood ratio test=0.59 on 1 df, p=0.4413
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD CIRBP
[1] 329
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.43 0.0424 0.201
strata=LOW 2 2 1.57 0.1199 0.201
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4492 1.5670 1.0100 0.445 0.657
Likelihood ratio test=0.2 on 1 df, p=0.6578
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD BRDT
============================
TCGA-COAD KIF4A
[1] 330
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.52 0.509 2.56
strata=LOW 3 3 1.48 1.551 2.56
Chisq= 2.6 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.688 5.408 1.172 1.44 0.15
Likelihood ratio test=2.47 on 1 df, p=0.1159
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD CPEB1
[1] 331
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.43 0.0424 0.201
strata=LOW 2 2 1.57 0.1199 0.201
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4492 1.5670 1.0100 0.445 0.657
Likelihood ratio test=0.2 on 1 df, p=0.6578
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD LINC01833
[1] 332
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.81 0.138 0.342
strata=LOW 5 5 4.19 0.159 0.342
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4307 1.5383 0.7412 0.581 0.561
Likelihood ratio test=0.35 on 1 df, p=0.5557
n= 9, number of events= 9
(17 observations deleted due to missingness)
============================
TCGA-COAD MAPKAP1
[1] 333
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.57 0.0911 0.192
strata=LOW 5 5 4.43 0.0734 0.192
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.3391 1.4036 0.7767 0.437 0.662
Likelihood ratio test=0.19 on 1 df, p=0.6607
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD ATF4
[1] 334
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.65 0.0267 0.0894
strata=LOW 2 2 2.35 0.0528 0.0894
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.2619 0.7696 0.8781 -0.298 0.766
Likelihood ratio test=0.09 on 1 df, p=0.7626
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD SLC7A11
[1] 335
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.98 9.31e-05 0.000242
strata=LOW 3 3 3.02 9.21e-05 0.000242
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.01448 0.98563 0.93137 -0.016 0.988
Likelihood ratio test=0 on 1 df, p=0.9876
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD EMC2
[1] 336
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.333 1.333 2
strata=LOW 2 2 2.667 0.167 2
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.215e+01 2.398e-10 4.566e+04 0 1
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD WWTR1
[1] 337
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.27 0.237 0.559
strata=LOW 2 2 2.73 0.197 0.559
Chisq= 0.6 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.8455 0.4293 1.1634 -0.727 0.467
Likelihood ratio test=0.59 on 1 df, p=0.4413
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD HSPA5
[1] 338
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.6 0.754 1.65
strata=LOW 2 2 3.4 0.576 1.65
Chisq= 1.7 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.3697 0.2542 1.1392 -1.202 0.229
Likelihood ratio test=1.78 on 1 df, p=0.1818
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD BEX1
[1] 339
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.52 0.0928 0.26
strata=LOW 2 2 2.48 0.0941 0.26
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5892 0.5548 1.1718 -0.503 0.615
Likelihood ratio test=0.27 on 1 df, p=0.6001
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PML
============================
TCGA-COAD MIR142
============================
TCGA-COAD AEBP2
[1] 340
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.33 0.0476 0.154
strata=LOW 2 2 1.67 0.0667 0.154
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4812 1.6180 1.2380 0.389 0.697
Likelihood ratio test=0.16 on 1 df, p=0.6913
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD GPAT4
[1] 341
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.4 0.0667 0.135
strata=LOW 4 4 3.6 0.0444 0.135
Chisq= 0.1 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.3429 1.4090 0.9368 0.366 0.714
Likelihood ratio test=0.14 on 1 df, p=0.712
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD CA9
[1] 342
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.167 0.43 2.88
strata=LOW 2 2 0.833 1.63 2.88
Chisq= 2.9 on 1 degrees of freedom, p= 0.09
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.168e+01 2.599e+09 2.943e+04 0.001 0.999
Likelihood ratio test=3.58 on 1 df, p=0.05836
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD STK11
[1] 343
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.5 0.0700 0.144
strata=LOW 4 4 4.5 0.0546 0.144
Chisq= 0.1 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.2922 0.7466 0.7736 -0.378 0.706
Likelihood ratio test=0.14 on 1 df, p=0.7041
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD TBK1
[1] 344
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.4 0.576 1.65
strata=LOW 4 4 2.6 0.754 1.65
Chisq= 1.7 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.370 3.934 1.139 1.202 0.229
Likelihood ratio test=1.78 on 1 df, p=0.1818
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD CDKN2A
[1] 345
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.38 0.112 0.365
strata=LOW 2 2 2.62 0.145 0.365
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.6766 0.5083 1.1392 -0.594 0.553
Likelihood ratio test=0.4 on 1 df, p=0.529
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD DCAF7
[1] 346
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 1.83 0.379 1.47
strata=LOW 2 2 1.17 0.595 1.47
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.097e+01 1.286e+09 2.928e+04 0.001 0.999
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD MTF1
[1] 347
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.43 0.0424 0.201
strata=LOW 2 2 1.57 0.1199 0.201
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4492 1.5670 1.0100 0.445 0.657
Likelihood ratio test=0.2 on 1 df, p=0.6578
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MEG8
[1] 348
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.55 1.370 2.04
strata=LOW 4 4 5.45 0.388 2.04
Chisq= 2 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.2510 0.2862 0.9283 -1.348 0.178
Likelihood ratio test=1.85 on 1 df, p=0.1734
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD CLTRN
[1] 349
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.17 0.595 1.47
strata=LOW 1 1 1.83 0.379 1.47
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.097e+01 7.775e-10 2.928e+04 -0.001 0.999
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD PARP11
[1] 350
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.19 0.00722 0.0192
strata=LOW 4 4 3.81 0.00985 0.0192
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.09896 1.10402 0.71460 0.138 0.89
Likelihood ratio test=0.02 on 1 df, p=0.8899
n= 9, number of events= 9
(15 observations deleted due to missingness)
============================
TCGA-COAD GABARAPL2
[1] 351
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.92 0.00238 0.0105
strata=LOW 1 1 1.08 0.00641 0.0105
Chisq= 0 on 1 degrees of freedom, p= 0.9
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.1285 0.8794 1.2535 -0.103 0.918
Likelihood ratio test=0.01 on 1 df, p=0.9178
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD CDKN1A
[1] 352
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.23 0.477 0.825
strata=LOW 3 3 3.77 0.156 0.825
Chisq= 0.8 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.073 0.342 1.235 -0.869 0.385
Likelihood ratio test=0.81 on 1 df, p=0.3677
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD NEDD4L
[1] 353
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.07 0.002051 0.00294
strata=LOW 7 7 6.93 0.000611 0.00294
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.04561 1.04667 0.84146 0.054 0.957
Likelihood ratio test=0 on 1 df, p=0.9566
n= 9, number of events= 9
(15 observations deleted due to missingness)
============================
TCGA-COAD AR
[1] 354
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.05 1.842 3.31
strata=LOW 3 3 4.95 0.765 3.31
Chisq= 3.3 on 1 degrees of freedom, p= 0.07
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.8395 0.1589 1.1393 -1.615 0.106
Likelihood ratio test=3.35 on 1 df, p=0.06722
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR20A
============================
TCGA-COAD HMOX1
[1] 355
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.88 0.160 0.985
strata=LOW 2 2 1.12 0.699 0.985
Chisq= 1 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.9671 2.6303 1.0107 0.957 0.339
Likelihood ratio test=0.88 on 1 df, p=0.3471
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD ZFP36
[1] 356
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.38 0.0335 0.141
strata=LOW 2 2 1.62 0.0909 0.141
Chisq= 0.1 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.3503 1.4194 0.9368 0.374 0.708
Likelihood ratio test=0.14 on 1 df, p=0.712
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR744
============================
TCGA-COAD CTSB
[1] 357
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.71 0.089 0.369
strata=LOW 3 3 2.29 0.222 0.369
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.4981 1.6456 0.8281 0.601 0.548
Likelihood ratio test=0.36 on 1 df, p=0.5493
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD AGPS
[1] 358
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.98 9.31e-05 0.000242
strata=LOW 3 3 3.02 9.21e-05 0.000242
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.01448 0.98563 0.93137 -0.016 0.988
Likelihood ratio test=0 on 1 df, p=0.9876
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MT1DP
[1] 359
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.167 0.43 2.88
strata=LOW 2 2 0.833 1.63 2.88
Chisq= 2.9 on 1 degrees of freedom, p= 0.09
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.168e+01 2.599e+09 2.943e+04 0.001 0.999
Likelihood ratio test=3.58 on 1 df, p=0.05836
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD SNX4
[1] 360
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.48 0.1800 0.297
strata=LOW 3 3 3.52 0.0759 0.297
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5493 0.5774 1.0198 -0.539 0.59
Likelihood ratio test=0.29 on 1 df, p=0.5922
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD NR4A1
[1] 361
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.3 1.247 2.38
strata=LOW 3 3 4.7 0.612 2.38
Chisq= 2.4 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.5841 0.2051 1.1292 -1.403 0.161
Likelihood ratio test=2.5 on 1 df, p=0.1141
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MFN2
[1] 362
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.8 0.133 4
strata=LOW 1 1 0.2 3.200 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.204e+01 3.739e+09 3.057e+04 0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD SELENOI
[1] 363
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.07 0.00215 0.00375
strata=LOW 4 4 3.93 0.00113 0.00375
Chisq= 0 on 1 degrees of freedom, p= 1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.05656 1.05819 0.92349 0.061 0.951
Likelihood ratio test=0 on 1 df, p=0.9511
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD AGAP2-AS1
[1] 364
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.72 0.0216 0.0979
strata=LOW 1 1 1.28 0.0626 0.0979
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.3695 0.6911 1.1865 -0.311 0.755
Likelihood ratio test=0.1 on 1 df, p=0.7492
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD TRIM46
[1] 365
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.27 0.0218 0.0739
strata=LOW 2 2 1.73 0.0410 0.0739
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.2739 1.3151 1.0107 0.271 0.786
Likelihood ratio test=0.07 on 1 df, p=0.7866
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD CYB5R1
[1] 366
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PARK7
[1] 367
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.67 0.167 0.615
strata=LOW 2 2 1.33 0.333 0.615
Chisq= 0.6 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.9406 2.5616 1.2403 0.758 0.448
Likelihood ratio test=0.62 on 1 df, p=0.4325
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD CARS1
[1] 368
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 6.69 0.0713 1.82
strata=LOW 1 1 0.31 1.5403 1.82
Chisq= 1.8 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.701 5.477 1.416 1.201 0.23
Likelihood ratio test=1.3 on 1 df, p=0.2547
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD NOX1
============================
TCGA-COAD VDR
[1] 369
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.77 0.156 0.485
strata=LOW 3 3 2.23 0.263 0.485
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.6321 1.8815 0.9220 0.686 0.493
Likelihood ratio test=0.48 on 1 df, p=0.4874
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PROK2
[1] 370
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.17 0.216 0.48
strata=LOW 3 3 3.83 0.179 0.48
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.6053 0.5459 0.8851 -0.684 0.494
Likelihood ratio test=0.49 on 1 df, p=0.483
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD FABP4
[1] 371
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.52 0.0495 0.175
strata=LOW 3 3 2.48 0.1102 0.175
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.3225 1.3806 0.7740 0.417 0.677
Likelihood ratio test=0.17 on 1 df, p=0.6797
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD ABCB10
[1] 372
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.367 1.0939 1.34
strata=LOW 5 5 5.633 0.0712 1.34
Chisq= 1.3 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.4979 0.2236 1.4164 -1.058 0.29
Likelihood ratio test=1.03 on 1 df, p=0.3107
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD CP
[1] 373
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.27 0.376 1.67
strata=LOW 3 3 1.73 0.926 1.67
Chisq= 1.7 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.394 4.033 1.164 1.198 0.231
Likelihood ratio test=1.69 on 1 df, p=0.1937
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR4735
============================
TCGA-COAD MIR130A
============================
TCGA-COAD TUG1
[1] 374
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.533 4.033 5.63
strata=LOW 4 4 5.467 0.393 5.63
Chisq= 5.6 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.195e+01 2.942e-10 2.380e+04 -0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR9-3HG
[1] 375
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.33 0.0249 0.0643
strata=LOW 4 4 3.67 0.0294 0.0643
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.1972 1.2180 0.7788 0.253 0.8
Likelihood ratio test=0.06 on 1 df, p=0.7994
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR196C
============================
TCGA-COAD IFNA21
============================
TCGA-COAD RP11-274B21.9
[1] 376
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.73 0.926 1.67
strata=LOW 3 3 4.27 0.376 1.67
Chisq= 1.7 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.395 0.248 1.164 -1.198 0.231
Likelihood ratio test=1.69 on 1 df, p=0.1937
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PVT1
[1] 377
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.92 0.612 1.78
strata=LOW 1 1 2.08 0.563 1.78
Chisq= 1.8 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.085e+01 8.800e-10 2.490e+04 -0.001 0.999
Likelihood ratio test=2.77 on 1 df, p=0.09589
n= 4, number of events= 4
(20 observations deleted due to missingness)
============================
TCGA-COAD MIR539
============================
TCGA-COAD IFNA2
============================
TCGA-COAD TFRC
[1] 378
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 1.83 0.379 1.47
strata=LOW 2 2 1.17 0.595 1.47
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.097e+01 1.286e+09 2.928e+04 0.001 0.999
Likelihood ratio test=2.2 on 1 df, p=0.1383
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD ALOX15B
[1] 379
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.4 0.0293 0.147
strata=LOW 2 2 1.6 0.0987 0.147
Chisq= 0.1 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.3505 1.4197 0.9188 0.381 0.703
Likelihood ratio test=0.14 on 1 df, p=0.7067
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MPC1
[1] 380
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.52 0.0759 0.297
strata=LOW 2 2 1.48 0.1800 0.297
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.5493 1.7321 1.0198 0.539 0.59
Likelihood ratio test=0.29 on 1 df, p=0.5922
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MTCH1
[1] 381
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.29 0.222 0.369
strata=LOW 5 5 5.71 0.089 0.369
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.4981 0.6077 0.8281 -0.601 0.548
Likelihood ratio test=0.36 on 1 df, p=0.5493
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR324
============================
TCGA-COAD SNHG14
[1] 382
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.28 2.323 3.21
strata=LOW 5 5 6.72 0.441 3.21
Chisq= 3.2 on 1 degrees of freedom, p= 0.07
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.5250 0.2176 0.9281 -1.643 0.1
Likelihood ratio test=2.72 on 1 df, p=0.09882
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD PDK4
[1] 383
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.48 0.1800 0.297
strata=LOW 3 3 3.52 0.0759 0.297
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5493 0.5774 1.0198 -0.539 0.59
Likelihood ratio test=0.29 on 1 df, p=0.5922
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD DUOX1
[1] 384
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.783 1.890 2.6
strata=LOW 4 4 5.217 0.284 2.6
Chisq= 2.6 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.766 0.171 1.235 -1.43 0.153
Likelihood ratio test=2.2 on 1 df, p=0.1382
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD LINC00886
[1] 385
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.34 0.3216 0.424
strata=LOW 6 6 6.66 0.0649 0.424
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5651 0.5683 0.8787 -0.643 0.52
Likelihood ratio test=0.39 on 1 df, p=0.5343
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD NF2
[1] 386
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.86 0.192 0.51
strata=LOW 4 4 3.14 0.237 0.51
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.6164 1.8523 0.8761 0.704 0.482
Likelihood ratio test=0.52 on 1 df, p=0.4702
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR149
============================
TCGA-COAD CYP4F8
[1] 387
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.45 0.0464 0.135
strata=LOW 4 4 3.55 0.0583 0.135
Chisq= 0.1 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.2873 1.3329 0.7856 0.366 0.715
Likelihood ratio test=0.13 on 1 df, p=0.7165
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD AKR1C1
[1] 388
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.6 0.754 1.65
strata=LOW 2 2 3.4 0.576 1.65
Chisq= 1.7 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.3697 0.2542 1.1392 -1.202 0.229
Likelihood ratio test=1.78 on 1 df, p=0.1818
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PRKCA
[1] 389
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.35 0.546 1.32
strata=LOW 5 5 3.65 0.501 1.32
Chisq= 1.3 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.199 3.318 1.105 1.085 0.278
Likelihood ratio test=1.48 on 1 df, p=0.2236
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD CD44
[1] 390
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 21 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.167 0.0128 0.0588
strata=LOW 1 1 0.833 0.0333 0.0588
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.3466 1.4142 1.4355 0.241 0.809
Likelihood ratio test=0.06 on 1 df, p=0.8096
n= 3, number of events= 3
(21 observations deleted due to missingness)
============================
TCGA-COAD FBXW7
[1] 391
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.533 4.033 5.63
strata=LOW 4 4 5.467 0.393 5.63
Chisq= 5.6 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.195e+01 2.942e-10 2.380e+04 -0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD YAP1
============================
TCGA-COAD MTOR
[1] 392
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.2 0.341 0.98
strata=LOW 4 4 2.8 0.509 0.98
Chisq= 1 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.8443 2.3263 0.8764 0.963 0.335
Likelihood ratio test=0.99 on 1 df, p=0.3197
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD RICTOR
[1] 393
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.48 0.0941 0.26
strata=LOW 3 3 2.52 0.0928 0.26
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.5892 1.8026 1.1718 0.503 0.615
Likelihood ratio test=0.27 on 1 df, p=0.6001
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD WIPI2
[1] 394
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.467 0.393 5.63
strata=LOW 2 2 0.533 4.033 5.63
Chisq= 5.6 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.195e+01 3.399e+09 2.380e+04 0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD IREB2
============================
TCGA-COAD GOT1
[1] 395
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.84 0.145 0.582
strata=LOW 3 3 2.16 0.325 0.582
Chisq= 0.6 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.6891 1.9919 0.9205 0.749 0.454
Likelihood ratio test=0.58 on 1 df, p=0.4481
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD CD82
[1] 396
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.633 0.0712 1.34
strata=LOW 1 1 0.367 1.0939 1.34
Chisq= 1.3 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.498 4.472 1.416 1.058 0.29
Likelihood ratio test=1.03 on 1 df, p=0.3107
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MAPK9
[1] 397
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 2.59 0.979 2.35
strata=LOW 6 6 4.41 0.576 2.35
Chisq= 2.3 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.067e+01 9.492e+08 1.968e+04 0.001 0.999
Likelihood ratio test=3.89 on 1 df, p=0.04852
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD LGMN
[1] 398
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.52 0.0759 0.297
strata=LOW 2 2 1.48 0.1800 0.297
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.5493 1.7321 1.0198 0.539 0.59
Likelihood ratio test=0.29 on 1 df, p=0.5922
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PARP2
[1] 399
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.07 0.371 1.18
strata=LOW 3 3 1.93 0.589 1.18
Chisq= 1.2 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.208 3.348 1.173 1.03 0.303
Likelihood ratio test=1.23 on 1 df, p=0.2675
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MIR16-1
============================
TCGA-COAD ATG4D
[1] 400
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.45 0.470 1.5
strata=LOW 4 4 2.55 0.818 1.5
Chisq= 1.5 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.046 2.845 0.888 1.178 0.239
Likelihood ratio test=1.49 on 1 df, p=0.2226
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD RBMS1
[1] 401
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.23 0.263 0.485
strata=LOW 3 3 3.77 0.156 0.485
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.6321 0.5315 0.9220 -0.686 0.493
Likelihood ratio test=0.48 on 1 df, p=0.4874
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD GSTZ1
[1] 402
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.52 0.0759 0.297
strata=LOW 2 2 1.48 0.1800 0.297
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.5493 1.7321 1.0198 0.539 0.59
Likelihood ratio test=0.29 on 1 df, p=0.5922
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD SRSF9
[1] 403
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.95 0.184 0.708
strata=LOW 3 3 2.05 0.446 0.708
Chisq= 0.7 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.6931 2.0000 0.8379 0.827 0.408
Likelihood ratio test=0.67 on 1 df, p=0.412
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD HIF1A
[1] 404
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.18 0.161 0.413
strata=LOW 3 3 3.82 0.176 0.413
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5028 0.6049 0.7891 -0.637 0.524
Likelihood ratio test=0.41 on 1 df, p=0.5213
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD FNDC3B
[1] 405
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.167 4.167 5
strata=LOW 5 5 5.833 0.119 5
Chisq= 5 on 1 degrees of freedom, p= 0.03
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.202e+01 2.736e-10 2.704e+04 -0.001 0.999
Likelihood ratio test=3.58 on 1 df, p=0.05836
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD RHEBP1
============================
TCGA-COAD PSEN1
[1] 406
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.92 0.607 0.917
strata=LOW 5 5 6.08 0.192 0.917
Chisq= 0.9 on 1 degrees of freedom, p= 0.3
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7767 0.4599 0.8298 -0.936 0.349
Likelihood ratio test=0.86 on 1 df, p=0.3546
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD ADIPOQ
[1] 407
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 28 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.65 0.0903 0.22
strata=LOW 5 5 4.35 0.0965 0.22
Chisq= 0.2 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.3474 1.4154 0.7444 0.467 0.641
Likelihood ratio test=0.22 on 1 df, p=0.6368
n= 9, number of events= 9
(28 observations deleted due to missingness)
============================
TCGA-COAD MUC1
[1] 408
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD CAV1
[1] 409
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.08 1.776 3.15
strata=LOW 4 4 5.92 0.623 3.15
Chisq= 3.1 on 1 degrees of freedom, p= 0.08
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.7929 0.1665 1.1356 -1.579 0.114
Likelihood ratio test=3.21 on 1 df, p=0.07303
n= 8, number of events= 8
(16 observations deleted due to missingness)
============================
TCGA-COAD SEC24B
[1] 410
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.48 0.1800 0.297
strata=LOW 3 3 3.52 0.0759 0.297
Chisq= 0.3 on 1 degrees of freedom, p= 0.6
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5493 0.5774 1.0198 -0.539 0.59
Likelihood ratio test=0.29 on 1 df, p=0.5922
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PRDX6
[1] 411
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.77 0.156 0.825
strata=LOW 2 2 1.23 0.477 0.825
Chisq= 0.8 on 1 degrees of freedom, p= 0.4
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.073 2.924 1.235 0.869 0.385
Likelihood ratio test=0.81 on 1 df, p=0.3677
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD TMEM161B-DT
[1] 412
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.783 0.0599 0.0824
strata=LOW 4 4 4.217 0.0111 0.0824
Chisq= 0.1 on 1 degrees of freedom, p= 0.8
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.3530 0.7026 1.2359 -0.286 0.775
Likelihood ratio test=0.08 on 1 df, p=0.7797
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PGD
[1] 413
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.833 0.119 5
strata=LOW 1 1 0.167 4.167 5
Chisq= 5 on 1 degrees of freedom, p= 0.03
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.202e+01 3.656e+09 2.704e+04 0.001 0.999
Likelihood ratio test=3.58 on 1 df, p=0.05836
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD RHOT1
[1] 414
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.32 0.3546 0.536
strata=LOW 4 4 4.68 0.0997 0.536
Chisq= 0.5 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.7222 0.4857 1.0075 -0.717 0.474
Likelihood ratio test=0.5 on 1 df, p=0.478
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD ACSL1
[1] 415
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.017 0.257 1.59
strata=LOW 2 2 0.983 1.051 1.59
Chisq= 1.6 on 1 degrees of freedom, p= 0.2
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 1.439 4.215 1.236 1.164 0.244
Likelihood ratio test=1.46 on 1 df, p=0.2262
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD NEDD4
[1] 416
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.4 0.2547 0.359
strata=LOW 5 5 5.6 0.0638 0.359
Chisq= 0.4 on 1 degrees of freedom, p= 0.5
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -0.5445 0.5801 0.9202 -0.592 0.554
Likelihood ratio test=0.33 on 1 df, p=0.5629
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD ELOVL5
[1] 417
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.783 1.890 2.6
strata=LOW 4 4 5.217 0.284 2.6
Chisq= 2.6 on 1 degrees of freedom, p= 0.1
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -1.766 0.171 1.235 -1.43 0.153
Likelihood ratio test=2.2 on 1 df, p=0.1382
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD YY1AP1
[1] 418
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.43 0.0547 0.155
strata=LOW 3 3 2.57 0.0732 0.155
Chisq= 0.2 on 1 degrees of freedom, p= 0.7
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 0.3625 1.4368 0.9256 0.392 0.695
Likelihood ratio test=0.16 on 1 df, p=0.6928
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
Display the results only for genes where a significant difference in survival has been reported.
significant_genes [1] "NQO1" "OIP5-AS1" "IDH2" "LCN2" "ATM" "NDRG1" "LINC00551" "MIB1" "AKT1S1" "PRKAA2" "LONP1"
[12] "MAPK1" "YTHDC2" "SMAD7" "PTPN14" "MIOX" "DUOX2" "KEAP1" "BRPF1" "ARHGEF26-AS1" "FOXO4" "HRAS"
[23] "PTEN" "SLC16A1-AS1" "MLST8" "PPARD" "SOCS1" "BACH1" "SMG9" "SREBF2" "ACOT1" "MFN2" "CYB5R1"
[34] "TUG1" "FBXW7" "WIPI2" "FNDC3B" "MUC1" "PGD" num_significant_genes <- length(significant_genes)
if (num_significant_genes > 0) {
for (i in 1 : num_significant_genes) {
project <- significant_projects[[i]]
gene <- significant_genes[[i]]
cat(project, gene, "\n\n")
gene_df <- construct_gene_df(gene, project)
fit <- compute_surival_fit(gene_df)
survival <- compute_survival_diff(gene_df)
cox <- compute_cox(gene_df)
print(survival)
cat("\n")
print(cox)
print(plot_survival(fit))
cat("\n\n============================\n\n")
}
}TCGA-COAD NQO1 Warning: Loglik converged before variable 1 ; coefficient may be infinite. Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD OIP5-AS1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD IDH2
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.9 0.926 3.86
strata=LOW 4 4 2.1 1.719 3.86
Chisq= 3.9 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.129e+01 1.754e+09 2.052e+04 0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD LCN2
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.1 1.719 3.86
strata=LOW 2 2 3.9 0.926 3.86
Chisq= 3.9 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.129e+01 5.700e-10 2.052e+04 -0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD ATM
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.452 5.294 6.98
strata=LOW 5 5 6.548 0.366 6.98
Chisq= 7 on 1 degrees of freedom, p= 0.008
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.158e+01 4.233e-10 1.775e+04 -0.001 0.999
Likelihood ratio test=6.09 on 1 df, p=0.0136
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD NDRG1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.467 0.393 5.63
strata=LOW 2 2 0.533 4.033 5.63
Chisq= 5.6 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.195e+01 3.399e+09 2.380e+04 0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD LINC00551
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MIB1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD AKT1S1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.8 0.133 4
strata=LOW 1 1 0.2 3.200 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.204e+01 3.739e+09 3.057e+04 0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PRKAA2
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.452 5.294 6.98
strata=LOW 5 5 6.548 0.366 6.98
Chisq= 7 on 1 degrees of freedom, p= 0.008
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.158e+01 4.233e-10 1.775e+04 -0.001 0.999
Likelihood ratio test=6.09 on 1 df, p=0.0136
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD LONP1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.35 0.419 4.26
strata=LOW 2 2 0.65 2.804 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.232e+01 4.923e+09 3.308e+04 0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MAPK1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.2 3.200 4
strata=LOW 4 4 4.8 0.133 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.204e+01 2.674e-10 3.057e+04 -0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD YTHDC2
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 4.19 1.14 4.2
strata=LOW 5 5 2.81 1.70 4.2
Chisq= 4.2 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.118e+01 1.579e+09 1.860e+04 0.001 0.999
Likelihood ratio test=6.09 on 1 df, p=0.0136
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD SMAD7
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PTPN14
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 0.962 4.318 6.62
strata=LOW 4 4 6.038 0.688 6.62
Chisq= 6.6 on 1 degrees of freedom, p= 0.01
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.242e+01 1.833e-10 2.728e+04 -0.001 0.999
Likelihood ratio test=7.11 on 1 df, p=0.007663
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD MIOX
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.8 0.133 4
strata=LOW 1 1 0.2 3.200 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.204e+01 3.739e+09 3.057e+04 0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD DUOX2
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 1.72 3.016 5.63
strata=LOW 3 3 5.28 0.984 5.63
Chisq= 5.6 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.172e+01 3.708e-10 2.077e+04 -0.001 0.999
Likelihood ratio test=7.11 on 1 df, p=0.007663
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD KEAP1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.85 0.706 5.05
strata=LOW 3 3 1.15 2.976 5.05
Chisq= 5.1 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.194e+01 3.381e+09 2.480e+04 0.001 0.999
Likelihood ratio test=5.99 on 1 df, p=0.01438
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD BRPF1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 6.038 0.688 6.62
strata=LOW 3 3 0.962 4.318 6.62
Chisq= 6.6 on 1 degrees of freedom, p= 0.01
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.242e+01 5.456e+09 2.728e+04 0.001 0.999
Likelihood ratio test=7.11 on 1 df, p=0.007663
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD ARHGEF26-AS1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 20 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.2 3.200 4
strata=LOW 4 4 4.8 0.133 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.204e+01 2.674e-10 3.057e+04 -0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(20 observations deleted due to missingness)
============================
TCGA-COAD FOXO4
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.35 0.419 4.26
strata=LOW 2 2 0.65 2.804 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.232e+01 4.923e+09 3.308e+04 0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD HRAS
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.8 0.133 4
strata=LOW 1 1 0.2 3.200 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.204e+01 3.739e+09 3.057e+04 0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PTEN
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD SLC16A1-AS1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.2 3.200 4
strata=LOW 4 4 4.8 0.133 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.204e+01 2.674e-10 3.057e+04 -0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD MLST8
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.85 0.706 5.05
strata=LOW 3 3 1.15 2.976 5.05
Chisq= 5.1 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.194e+01 3.381e+09 2.480e+04 0.001 0.999
Likelihood ratio test=5.99 on 1 df, p=0.01438
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD PPARD
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.15 2.976 5.05
strata=LOW 3 3 4.85 0.706 5.05
Chisq= 5.1 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.194e+01 2.957e-10 2.480e+04 -0.001 0.999
Likelihood ratio test=5.99 on 1 df, p=0.01438
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD SOCS1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.8 0.133 4
strata=LOW 1 1 0.2 3.200 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.204e+01 3.739e+09 3.057e+04 0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD BACH1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.9 0.926 3.86
strata=LOW 4 4 2.1 1.719 3.86
Chisq= 3.9 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.129e+01 1.754e+09 2.052e+04 0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD SMG9
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.467 0.393 5.63
strata=LOW 2 2 0.533 4.033 5.63
Chisq= 5.6 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.195e+01 3.399e+09 2.380e+04 0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD SREBF2
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 1.72 3.016 5.63
strata=LOW 3 3 5.28 0.984 5.63
Chisq= 5.6 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.172e+01 3.708e-10 2.077e+04 -0.001 0.999
Likelihood ratio test=7.11 on 1 df, p=0.007663
n= 7, number of events= 7
(17 observations deleted due to missingness)
============================
TCGA-COAD ACOT1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.85 0.706 5.05
strata=LOW 3 3 1.15 2.976 5.05
Chisq= 5.1 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.194e+01 3.381e+09 2.480e+04 0.001 0.999
Likelihood ratio test=5.99 on 1 df, p=0.01438
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MFN2
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.8 0.133 4
strata=LOW 1 1 0.2 3.200 4
Chisq= 4 on 1 degrees of freedom, p= 0.05
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.204e+01 3.739e+09 3.057e+04 0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD CYB5R1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD TUG1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.533 4.033 5.63
strata=LOW 4 4 5.467 0.393 5.63
Chisq= 5.6 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.195e+01 2.942e-10 2.380e+04 -0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD FBXW7
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.533 4.033 5.63
strata=LOW 4 4 5.467 0.393 5.63
Chisq= 5.6 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.195e+01 2.942e-10 2.380e+04 -0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD WIPI2
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.467 0.393 5.63
strata=LOW 2 2 0.533 4.033 5.63
Chisq= 5.6 on 1 degrees of freedom, p= 0.02
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.195e+01 3.399e+09 2.380e+04 0.001 0.999
Likelihood ratio test=5.42 on 1 df, p=0.01995
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD FNDC3B
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.167 4.167 5
strata=LOW 5 5 5.833 0.119 5
Chisq= 5 on 1 degrees of freedom, p= 0.03
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.202e+01 2.736e-10 2.704e+04 -0.001 0.999
Likelihood ratio test=3.58 on 1 df, p=0.05836
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
TCGA-COAD MUC1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.65 2.804 4.26
strata=LOW 3 3 4.35 0.419 4.26
Chisq= 4.3 on 1 degrees of freedom, p= 0.04
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW -2.232e+01 2.031e-10 3.308e+04 -0.001 0.999
Likelihood ratio test=4.61 on 1 df, p=0.03188
n= 5, number of events= 5
(19 observations deleted due to missingness)
============================
TCGA-COAD PGD
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 18 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.833 0.119 5
strata=LOW 1 1 0.167 4.167 5
Chisq= 5 on 1 degrees of freedom, p= 0.03
Call:
coxph(formula = Surv(overall_survival, deceased) ~ strata, data = gene_df)
coef exp(coef) se(coef) z p
strataLOW 2.202e+01 3.656e+09 2.704e+04 0.001 0.999
Likelihood ratio test=3.58 on 1 df, p=0.05836
n= 6, number of events= 6
(18 observations deleted due to missingness)
============================
De La Salle University, Manila, Philippines, gonzales.markedward@gmail.com↩︎
De La Salle University, Manila, Philippines, anish.shrestha@dlsu.edu.ph↩︎
---
title: "Survival Analysis"
subtitle: "Colorectal Cancer | Ferroptosis | Unique Genes per RCD Type | Gene Expression of Tumor Samples"
author: 
  - Mark Edward M. Gonzales^[De La Salle University, Manila, Philippines, gonzales.markedward@gmail.com]
  - Dr. Anish M.S. Shrestha^[De La Salle University, Manila, Philippines, anish.shrestha@dlsu.edu.ph]
output: html_notebook
---

## I. Preliminaries

### Loading libraries

```{r, warning=FALSE, message=FALSE}
library("tidyverse")
library("tibble")
library("msigdbr")
library("ggplot2")
library("TCGAbiolinks")
library("RNAseqQC")
library("DESeq2")
library("ensembldb")
library("purrr")
library("magrittr")
library("vsn")
library("matrixStats")
library("dplyr")
library("grex")
library("survminer")
library("survival")
```

## II. Downloading the TCGA gene expression data 

Create a function for downloading TCGA gene expression data. 

For more detailed documentation, refer to `2. Differential Gene Expression Analysis - TCGA.Rmd`.

```{r}
GDC_DIR = "../data/public/GDCdata"

query_and_filter_samples <- function(project) {
  query_tumor <- GDCquery(
    project = project,
    data.category = "Transcriptome Profiling",
    data.type = "Gene Expression Quantification",
    experimental.strategy = "RNA-Seq",
    workflow.type = "STAR - Counts",
    access = "open",
    sample.type = "Primary Tumor"
  )
  tumor <- getResults(query_tumor)

  query_normal <- GDCquery(
    project = project,
    data.category = "Transcriptome Profiling",
    data.type = "Gene Expression Quantification",
    experimental.strategy = "RNA-Seq",
    workflow.type = "STAR - Counts",
    access = "open",
    sample.type = "Solid Tissue Normal"
  )
  normal <- getResults(query_normal)

  submitter_ids <- inner_join(tumor, normal, by = "cases.submitter_id") %>%
    dplyr::select(cases.submitter_id)
  tumor <- tumor %>%
    dplyr::filter(cases.submitter_id %in% submitter_ids$cases.submitter_id)
  normal <- normal %>%
    dplyr::filter(cases.submitter_id %in% submitter_ids$cases.submitter_id)

  samples <- rbind(tumor, normal)
  unique(samples$sample_type)

  query_project <- GDCquery(
    project = project,
    data.category = "Transcriptome Profiling",
    data.type = "Gene Expression Quantification",
    experimental.strategy = "RNA-Seq",
    workflow.type = "STAR - Counts",
    access = "open",
    sample.type = c("Solid Tissue Normal", "Primary Tumor"),
    barcode = as.list(samples$sample.submitter_id)
  )

  # If this is your first time running this notebook (i.e., you have not yet downloaded the results of the query in the previous block),
  # uncomment the code block below

  # GDCdownload(
  #   query_coad,
  #   directory = GDC_DIR
  # )

  return(list(samples = samples, query_project = query_project))
}
```

Download the TCGA gene expression data for colorectal cancer (TCGA-COAD).

```{r, echo = TRUE, message = FALSE, results="hide"}
projects <- c("TCGA-COAD")

with_results_projects <- c()

samples <- list()
project_data <- list()

for (project in projects) {
  result <- tryCatch(
    {
      result <- query_and_filter_samples(project)
      samples[[project]] <- result$samples
      project_data[[project]] <- result$query_project

      with_results_projects <- c(with_results_projects, project)
    },
    error = function(e) {

    }
  )
}
```

Running the code block above should generate and populate a directory named `GDCdata`.

## III. Data preprocessing

Construct the RNA-seq count matrix for each cancer type.

```{r, echo = TRUE, message = FALSE, results="hide"}
tcga_data <- list()
tcga_matrix <- list()

projects <- with_results_projects
for (project in projects) {
  tcga_data[[project]] <- GDCprepare(
    project_data[[project]], 
    directory = GDC_DIR,
    summarizedExperiment = TRUE
  )
}
```

```{r}
for (project in projects) {
  count_matrix <- assay(tcga_data[[project]], "unstranded")

  # Remove duplicate entries
  count_matrix_df <- data.frame(count_matrix)
  count_matrix_df <- count_matrix_df[!duplicated(count_matrix_df), ]
  count_matrix <- data.matrix(count_matrix_df)
  rownames(count_matrix) <- cleanid(rownames(count_matrix))
  count_matrix <- count_matrix[!(duplicated(rownames(count_matrix)) | duplicated(rownames(count_matrix), fromLast = TRUE)), ]

  tcga_matrix[[project]] <- count_matrix
}
```
Format the `samples` table so that it can be fed as input to DESeq2.

```{r}
for (project in projects) {
  rownames(samples[[project]]) <- samples[[project]]$cases
  samples[[project]] <- samples[[project]] %>%
    dplyr::select(case = "cases.submitter_id", type = "sample_type")
  samples[[project]]$type <- str_replace(samples[[project]]$type, "Solid Tissue Normal", "normal")
  samples[[project]]$type <- str_replace(samples[[project]]$type, "Primary Tumor", "tumor")
}
```

DESeq2 requires the row names of `samples` should be identical to the column names of `count_matrix`.

```{r, echo = TRUE, results="hide"}
for (project in projects) {
  colnames(tcga_matrix[[project]]) <- gsub(x = colnames(tcga_matrix[[project]]), pattern = "\\.", replacement = "-")
  tcga_matrix[[project]] <- tcga_matrix[[project]][, rownames(samples[[project]])]

  # Sanity check
  print(all(colnames(tcga_matrix[[project]]) == rownames(samples[[project]])))
}
```

## IV. Differential gene expression analysis

For more detailed documentation on obtaining the gene set, refer to `7. Differential Gene Expression Analysis - TCGA - Pan-cancer - Unique Genes.Rmd`.

```{r}
RCDdb <- "../data/public/rcd-gene-list/unique-genes/necroptosis-ferroptosis-pyroptosis/"
```

Write utility functions for filtering the gene sets, performing differential gene expression analysis, plotting the results, and performing variance-stabilizing transformation.

```{r}
filter_gene_set_and_perform_dgea <- function(genes) {
  tcga_rcd <- list()

  for (project in projects) {
    rownames(genes) <- genes$gene_id
    tcga_rcd[[project]] <- tcga_matrix[[project]][rownames(tcga_matrix[[project]]) %in% genes$gene_id, ]
    tcga_rcd[[project]] <- tcga_rcd[[project]][, rownames(samples[[project]])]
  }

  dds_rcd <- list()
  res_rcd <- list()

  for (project in projects) {
    print(project)
    print("=============")
    dds <- DESeqDataSetFromMatrix(
      countData = tcga_rcd[[project]],
      colData = samples[[project]],
      design = ~type
    )
    dds <- filter_genes(dds, min_count = 10)
    dds$type <- relevel(dds$type, ref = "normal")
    dds_rcd[[project]] <- DESeq(dds)
    res_rcd[[project]] <- results(dds_rcd[[project]])
  }

  deseq.bbl.data <- list()

  for (project in projects) {
    deseq.results <- res_rcd[[project]]
    deseq.bbl.data[[project]] <- data.frame(
      row.names = rownames(deseq.results),
      baseMean = deseq.results$baseMean,
      log2FoldChange = deseq.results$log2FoldChange,
      lfcSE = deseq.results$lfcSE,
      stat = deseq.results$stat,
      pvalue = deseq.results$pvalue,
      padj = deseq.results$padj,
      cancer_type = project,
      gene_symbol = genes[rownames(deseq.results), "gene"]
    )
  }

  deseq.bbl.data.combined <- bind_rows(deseq.bbl.data)
  deseq.bbl.data.combined <- dplyr::filter(deseq.bbl.data.combined, abs(log2FoldChange) >= 1.5 & padj < 0.05)

  return(deseq.bbl.data.combined)
}
```

```{r}
plot_dgea <- function(deseq.bbl.data.combined) {
  sizes <- c("<10^-15" = 4, "10^-10" = 3, "10^-5" = 2, "0.05" = 1)

  deseq.bbl.data.combined <- deseq.bbl.data.combined %>%
    mutate(fdr_category = cut(padj,
      breaks = c(-Inf, 1e-15, 1e-10, 1e-5, 0.05),
      labels = c("<10^-15", "10^-10", "10^-5", "0.05"),
      right = FALSE
    ))

  top_genes <- deseq.bbl.data.combined %>%
    group_by(cancer_type) %>%
    mutate(rank = rank(-abs(log2FoldChange))) %>%
    dplyr::filter(rank <= 10) %>%
    ungroup()

  ggplot(top_genes, aes(y = cancer_type, x = gene_symbol, size = fdr_category, fill = log2FoldChange)) +
    geom_point(alpha = 0.5, shape = 21, color = "black") +
    scale_size_manual(values = sizes) +
    scale_fill_gradient2(low = "blue", mid = "white", high = "red", limits = c(min(deseq.bbl.data.combined$log2FoldChange), max(deseq.bbl.data.combined$log2FoldChange))) +
    theme_minimal() +
    theme(
      axis.text.x = element_text(size = 9, angle = 90, hjust = 1)
    ) +
    theme(legend.position = "bottom") +
    theme(legend.position = "bottom") +
    labs(size = "Adjusted p-value", fill = "log2 FC", y = "Cancer type", x = "Gene")
}
```

```{r}
perform_vsd <- function(genes) {
  tcga_rcd <- list()

  for (project in projects) {
    rownames(genes) <- genes$gene_id
    tcga_rcd[[project]] <- tcga_matrix[[project]][rownames(tcga_matrix[[project]]) %in% genes$gene_id, ]
    tcga_rcd[[project]] <- tcga_rcd[[project]][, rownames(samples[[project]])]
  }

  vsd_rcd <- list()

  for (project in projects) {
    print(project)
    print("=============")
    dds <- DESeqDataSetFromMatrix(
      countData = tcga_rcd[[project]],
      colData = samples[[project]],
      design = ~type
    )
    dds <- filter_genes(dds, min_count = 10)

    # Perform variance stabilization
    dds <- estimateSizeFactors(dds)
    nsub <- sum(rowMeans(counts(dds, normalized = TRUE)) > 10)
    vsd <- vst(dds, nsub = nsub)
    vsd_rcd[[project]] <- assay(vsd)
  }

  return(vsd_rcd)
}
```


#### Ferroptosis

Fetch the gene set of interest.

```{r}
genes <- read.csv(paste0(RCDdb, "Ferroptosis.csv"))
print(genes)
genes$gene_id <- cleanid(genes$gene_id)
genes <- distinct(genes, gene_id, .keep_all = TRUE)
genes <- subset(genes, gene_id != "")
genes
```

Filter the genes to include only those in the gene set of interest, and then perform differential gene expression analysis.

```{r}
deseq.bbl.data.combined <- filter_gene_set_and_perform_dgea(genes)
deseq.bbl.data.combined
```

Plot the results.

```{r}
plot_dgea(deseq.bbl.data.combined)
```
Perform variance-stabilizing transformation for further downstream analysis (i.e., for survival analysis).

```{r, warning=FALSE}
vsd <- perform_vsd(genes)
```

## V. Downloading the clinical data

Download clinical data from TCGA, and perform some preprocessing:
- The `deceased` column should be `FALSE` if the patient is alive and `TRUE` otherwise
- The `overall_survival` column should reflect the follow-up time if the patient is alive and the days to death otherwise

```{r}
download_clinical_data <- function(project) {
  clinical_data <- GDCquery_clinic(project)
  clinical_data$deceased <- ifelse(clinical_data$vital_status == "Alive", FALSE, TRUE)
  clinical_data$overall_survival <- ifelse(clinical_data$vital_status == "Alive",
    clinical_data$days_to_last_follow_up,
    clinical_data$days_to_death
  )

  return(clinical_data)
}
```

```{r}
tcga_clinical <- list()
for (project in projects) {
  tcga_clinical[[project]] <- download_clinical_data(project)
}
```

## VI. Performing survival analysis

Write utility functions for performing survival analysis.


```{r}
construct_gene_df <- function(gene_of_interest, project) {
  gene_df <- vsd[[project]] %>%
    as.data.frame() %>%
    rownames_to_column(var = "gene_id") %>%
    gather(key = "case_id", value = "counts", -gene_id) %>%
    left_join(., genes, by = "gene_id") %>%
    dplyr::filter(gene == gene_of_interest) %>%
    dplyr::filter(case_id %in% rownames(samples[[project]] %>% dplyr::filter(type == "tumor")))

  q1 <- quantile(gene_df$counts, probs = 0.25)
  q3 <- quantile(gene_df$counts, probs = 0.75)
  gene_df$strata <- ifelse(gene_df$counts >= q3, "HIGH", ifelse(gene_df$counts <= q1, "LOW", "MIDDLE"))
  gene_df <- gene_df %>% dplyr::filter(strata %in% c("LOW", "HIGH"))
  gene_df$case_id <- paste0(sapply(strsplit(as.character(gene_df$case_id), "-"), `[`, 1), '-',
                          sapply(strsplit(as.character(gene_df$case_id), "-"), `[`, 2), '-', 
                          sapply(strsplit(as.character(gene_df$case_id), "-"), `[`, 3))
  gene_df <- merge(gene_df, tcga_clinical[[project]], by.x = "case_id", by.y = "submitter_id")
  
  return(gene_df)
}
```

```{r}
compute_surival_fit <- function(gene_df) {
  return (survfit(Surv(overall_survival, deceased) ~ strata, data = gene_df))
}
```

```{r}
compute_cox <- function(gene_df) {
  return (coxph(Surv(overall_survival, deceased) ~ strata, data=gene_df))
}
```

```{r}
plot_survival <- function(fit) {
  return(ggsurvplot(fit,
    data = gene_df,
    pval = T,
    risk.table = T,
    risk.table.height = 0.3
  ))
}
```

```{r}
compute_survival_diff <- function(gene_df) {
  return(survdiff(Surv(overall_survival, deceased) ~ strata, data = gene_df))
}
```

Perform survival analysis by testing for the difference in the Kaplan-Meier curves using the G-rho family of Harrington and Fleming tests: https://rdrr.io/cran/survival/man/survdiff.html

```{r}
significant_projects <- c()
significant_genes <- c()

ctr <- 1
for (project in projects) {
  for (gene in c(genes$gene)) {
    cat(project, gene, "\n\n")
    error <- tryCatch (
      {
        gene_df <- construct_gene_df(gene, project)
      },
      error = function(e) {
        cat("\n\n============================\n\n")
        e
      }
    )
    
    if(inherits(error, "error")) next

    if (nrow(gene_df) > 0) {
      fit <- compute_surival_fit(gene_df)
      tryCatch (
        {
          survival <- compute_survival_diff(gene_df)
          cox <- compute_cox(gene_df)
          print(ctr)
          ctr <- ctr + 1
          print(survival)
          cat("\n")
          print(cox)
          print(plot_survival(fit))
          if (pchisq(survival$chisq, length(survival$n)-1, lower.tail = FALSE) < 0.05) {
            significant_projects <- c(significant_projects, project)
            significant_genes <- c(significant_genes, gene)
          }
        },
        error = function(e) {
        }
      )
      
    }
    
    cat("\n\n============================\n\n")
  }
}
```

Display the results only for genes where a significant difference in survival has been reported.

```{r}
significant_genes
```

```{r}
num_significant_genes <- length(significant_genes)

if (num_significant_genes > 0) {
  for (i in 1 : num_significant_genes) {
    project <- significant_projects[[i]]
    gene <- significant_genes[[i]]
    
    cat(project, gene, "\n\n")
    gene_df <- construct_gene_df(gene, project)
    
    fit <- compute_surival_fit(gene_df)
    survival <- compute_survival_diff(gene_df)
    cox <- compute_cox(gene_df)
    print(survival)
    cat("\n")
    print(cox)
    print(plot_survival(fit))
    
    cat("\n\n============================\n\n")
  } 
}
```