Survival Analysis
Colorectal Cancer | Ferroptosis | Unique Genes per RCD Type | Gene Expression of Normal 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$days_to_death
)
return(clinical_data)
}tcga_clinical <- list()
for (project in projects) {
tcga_clinical[[project]] <- download_clinical_data(project)
}VI. Performing survival analysis
Write utility functions for performing survival analysis.
construct_gene_df <- function(gene_of_interest, project) {
gene_df <- vsd[[project]] %>%
as.data.frame() %>%
rownames_to_column(var = "gene_id") %>%
gather(key = "case_id", value = "counts", -gene_id) %>%
left_join(., genes, by = "gene_id") %>%
dplyr::filter(gene == gene_of_interest) %>%
dplyr::filter(case_id %in% rownames(samples[[project]] %>% dplyr::filter(type == "normal")))
q1 <- quantile(gene_df$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
Our genes of interest are the differentially expressed genes.
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=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3 7.57e-06 1.56e-05
strata=LOW 4 4 4 5.66e-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 0.996737 0.828416 -0.004 0.997
Likelihood ratio test=0 on 1 df, p=0.9969
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD TFAM
[1] 2
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.3 0.0216 0.0544
strata=LOW 4 4 3.7 0.0251 0.0544
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 0.1798 1.1970 0.7718 0.233 0.816
Likelihood ratio test=0.05 on 1 df, p=0.8152
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD CREB5
[1] 3
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.383 0.0273 0.302
strata=LOW 1 1 0.617 0.2383 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 1.9434 1.2307 0.54 0.589
Likelihood ratio test=0.27 on 1 df, p=0.6049
n= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD NOS2
[1] 4
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.3 0.146 0.283
strata=LOW 4 4 4.7 0.103 0.283
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 -0.4083 0.6648 0.7723 -0.529 0.597
Likelihood ratio test=0.28 on 1 df, p=0.5947
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD HULC
[1] 5
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD PLXNB2
[1] 6
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD KIF20A
[1] 7
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.39 0.358 1.02
strata=LOW 5 5 3.61 0.535 1.02
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 0.7416 2.0994 0.7486 0.991 0.322
Likelihood ratio test=1.02 on 1 df, p=0.3124
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD TIMP1
[1] 8
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 6.15 0.00354 0.0172
strata=LOW 2 2 1.85 0.01176 0.0172
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 0.1145 1.1213 0.8720 0.131 0.896
Likelihood ratio test=0.02 on 1 df, p=0.8962
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD MIR615
============================
TCGA-COAD MIR93
============================
TCGA-COAD ENO3
[1] 9
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD MMD
[1] 10
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD NQO1
[1] 11
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.57 0.540 1.46
strata=LOW 5 5 3.43 0.719 1.46
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 0.9880 2.6858 0.8489 1.164 0.245
Likelihood ratio test=1.5 on 1 df, p=0.2206
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD MARCHF5
[1] 12
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3 0.334 0.61
strata=LOW 5 5 6 0.167 0.61
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 -0.6025 0.5474 0.7816 -0.771 0.441
Likelihood ratio test=0.6 on 1 df, p=0.4376
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD JUN
[1] 13
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD ALDH3A2
[1] 14
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.833 0.0333 0.0588
strata=LOW 2 2 2.167 0.0128 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 0.7071 1.4355 -0.241 0.809
Likelihood ratio test=0.06 on 1 df, p=0.8096
n= 3, number of events= 3
(19 observations deleted due to missingness)
============================
TCGA-COAD ALOX5
[1] 15
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.22 1.424 2.7
strata=LOW 4 4 5.78 0.547 2.7
Chisq= 2.7 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 -1.698 0.183 1.143 -1.486 0.137
Likelihood ratio test=2.81 on 1 df, p=0.09364
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD PARP9
[1] 16
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD GLRX5
[1] 17
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.83 0.00611 0.0158
strata=LOW 4 4 4.17 0.00708 0.0158
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 -0.0928 0.9114 0.7388 -0.126 0.9
Likelihood ratio test=0.02 on 1 df, p=0.8997
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD METTL14
[1] 18
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.38 0.0878 0.24
strata=LOW 3 3 3.62 0.1063 0.24
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 -0.4116 0.6626 0.8453 -0.487 0.626
Likelihood ratio test=0.25 on 1 df, p=0.6174
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD TOR2A
[1] 19
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.91 0.619 1.03
strata=LOW 4 4 5.09 0.233 1.03
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 -0.9149 0.4005 0.9283 -0.986 0.324
Likelihood ratio test=1 on 1 df, p=0.3178
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD PARP14
[1] 20
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR130B
============================
TCGA-COAD CERS6-AS1
============================
TCGA-COAD NFS1
[1] 21
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD SLC3A2
[1] 22
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=10, 12 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.9 0.00261 0.00477
strata=LOW 6 6 6.1 0.00167 0.00477
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 -0.04716 0.95393 0.68317 -0.069 0.945
Likelihood ratio test=0 on 1 df, p=0.945
n= 10, number of events= 10
(12 observations deleted due to missingness)
============================
TCGA-COAD ZFAS1
[1] 23
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.1 0.00499 0.0079
strata=LOW 5 5 4.9 0.00214 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 1.0812 0.8787 0.089 0.929
Likelihood ratio test=0.01 on 1 df, p=0.9289
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD PANX1
============================
TCGA-COAD HSPB1
[1] 24
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD CREB1
[1] 25
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4 5.68e-06 1.35e-05
strata=LOW 4 4 4 5.66e-06 1.35e-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 -0.002835 0.997169 0.771518 -0.004 0.997
Likelihood ratio test=0 on 1 df, p=0.9971
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD EZH2
[1] 26
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.73 0.197 0.559
strata=LOW 3 3 2.27 0.237 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 2.3292 1.1634 0.727 0.467
Likelihood ratio test=0.59 on 1 df, p=0.4413
n= 5, number of events= 5
(17 observations deleted due to missingness)
============================
TCGA-COAD SLC40A1
[1] 27
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=10, 12 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.26 0.170 0.294
strata=LOW 6 6 6.74 0.082 0.294
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 -0.3866 0.6794 0.7171 -0.539 0.59
Likelihood ratio test=0.29 on 1 df, p=0.5908
n= 10, number of events= 10
(12 observations deleted due to missingness)
============================
TCGA-COAD PAQR3
[1] 28
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR545
============================
TCGA-COAD MIR6077
============================
TCGA-COAD MIR424
============================
TCGA-COAD NOX5
[1] 29
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD DHODH
[1] 30
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.217 0.0111 0.0824
strata=LOW 1 1 0.783 0.0599 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 0.353 1.423 1.236 0.286 0.775
Likelihood ratio test=0.08 on 1 df, p=0.7797
n= 5, number of events= 5
(17 observations deleted due to missingness)
============================
TCGA-COAD PTPN18
[1] 31
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD IARS1
[1] 32
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD IL4R
[1] 33
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.95 0.00076 0.00182
strata=LOW 4 4 4.05 0.00074 0.00182
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 -0.03336 0.96719 0.78130 -0.043 0.966
Likelihood ratio test=0 on 1 df, p=0.9659
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD SENP1
[1] 34
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD IFNA16
============================
TCGA-COAD SOX2
[1] 35
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD LIFR
[1] 36
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR199A2
============================
TCGA-COAD COX4I2
[1] 37
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD ATF2
[1] 38
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD ABCC5
[1] 39
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.18 0.00803 0.03
strata=LOW 2 2 1.82 0.01850 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 1.1739 0.9273 0.173 0.863
Likelihood ratio test=0.03 on 1 df, p=0.8635
n= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD CCDC6
============================
TCGA-COAD OTUB1
[1] 40
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.79 0.01629 0.0279
strata=LOW 5 5 5.21 0.00871 0.0279
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 -0.1294 0.8786 0.7754 -0.167 0.867
Likelihood ratio test=0.03 on 1 df, p=0.8679
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD ALOXE3
[1] 41
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=11, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 5.44 0.0578 0.128
strata=LOW 5 5 5.56 0.0566 0.128
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 -0.2320 0.7930 0.6491 -0.357 0.721
Likelihood ratio test=0.13 on 1 df, p=0.719
n= 11, number of events= 11
(15 observations deleted due to missingness)
============================
TCGA-COAD SCP2
[1] 42
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD PHKG2
[1] 43
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MTDH
[1] 44
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=10, 12 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 3.65 1.512 2.88
strata=LOW 4 4 6.35 0.869 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 -1.3159 0.2682 0.8274 -1.59 0.112
Likelihood ratio test=2.95 on 1 df, p=0.08568
n= 10, number of events= 10
(12 observations deleted due to missingness)
============================
TCGA-COAD ACO1
[1] 45
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=10, 12 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 7 7 7.76 0.0737 0.362
strata=LOW 3 3 2.24 0.2547 0.362
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 0.4418 1.5555 0.7401 0.597 0.551
Likelihood ratio test=0.34 on 1 df, p=0.5587
n= 10, number of events= 10
(12 observations deleted due to missingness)
============================
TCGA-COAD MIR137
============================
TCGA-COAD OIP5-AS1
[1] 46
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.01 0.202 0.624
strata=LOW 5 5 3.99 0.253 0.624
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 0.6683 1.9508 0.8595 0.777 0.437
Likelihood ratio test=0.65 on 1 df, p=0.4195
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD MIR494
============================
TCGA-COAD MLLT1
[1] 47
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 7 7 7.88 0.0973 0.888
strata=LOW 2 2 1.12 0.6814 0.888
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 0.8415 2.3199 0.9190 0.916 0.36
Likelihood ratio test=0.78 on 1 df, p=0.3786
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD MIR19B1
============================
TCGA-COAD RPTOR
[1] 48
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 7.098 0.17 1.74
strata=LOW 2 2 0.902 1.34 1.74
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 1.253 3.499 1.009 1.242 0.214
Likelihood ratio test=1.45 on 1 df, p=0.2278
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD GCH1
[1] 49
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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 4 4 5.017 0.206 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= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD PARP16
[1] 50
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD MIR9-3
============================
TCGA-COAD CISD3
[1] 51
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.08 0.00120 0.00338
strata=LOW 4 4 3.92 0.00156 0.00338
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 0.04302 1.04396 0.73990 0.058 0.954
Likelihood ratio test=0 on 1 df, p=0.9537
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD USP35
[1] 52
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=10, 12 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 6.93 0.126 0.526
strata=LOW 4 4 3.07 0.285 0.526
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 0.5588 1.7485 0.7795 0.717 0.473
Likelihood ratio test=0.52 on 1 df, p=0.4703
n= 10, number of events= 10
(12 observations deleted due to missingness)
============================
TCGA-COAD PRKAA1
[1] 53
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.59 1.258 1.9
strata=LOW 5 5 6.41 0.311 1.9
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 -1.2154 0.2966 0.9303 -1.306 0.191
Likelihood ratio test=1.74 on 1 df, p=0.1865
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD MAPK14
[1] 54
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=10, 12 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.52 0.869 1.38
strata=LOW 6 6 7.48 0.293 1.38
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 -0.8760 0.4165 0.7698 -1.138 0.255
Likelihood ratio test=1.31 on 1 df, p=0.2526
n= 10, number of events= 10
(12 observations deleted due to missingness)
============================
TCGA-COAD GRIA3
[1] 55
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.06 0.285 0.473
strata=LOW 5 5 5.94 0.147 0.473
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 -0.4880 0.6139 0.7159 -0.682 0.495
Likelihood ratio test=0.46 on 1 df, p=0.4974
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD KDM5C
[1] 56
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD DECR1
[1] 57
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.86 0.00666 0.0131
strata=LOW 4 4 4.14 0.00461 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 0.90969 0.82764 -0.114 0.909
Likelihood ratio test=0.01 on 1 df, p=0.909
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD VCP
[1] 58
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR129-1
============================
TCGA-COAD PARP10
[1] 59
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.34 0.131 0.301
strata=LOW 3 3 3.66 0.120 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 0.6225 0.8721 -0.543 0.587
Likelihood ratio test=0.31 on 1 df, p=0.5787
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD ULK2
[1] 60
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.217 0.0111 0.0824
strata=LOW 1 1 0.783 0.0599 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 0.353 1.423 1.236 0.286 0.775
Likelihood ratio test=0.08 on 1 df, p=0.7797
n= 5, number of events= 5
(17 observations deleted due to missingness)
============================
TCGA-COAD CISD1
[1] 61
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.18 0.00803 0.03
strata=LOW 2 2 1.82 0.01850 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 1.1739 0.9273 0.173 0.863
Likelihood ratio test=0.03 on 1 df, p=0.8635
n= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR147A
============================
TCGA-COAD BBOX1-AS1
[1] 62
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD RB1
[1] 63
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD TTPA
[1] 64
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD CDC25A
[1] 65
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD PCAT1
[1] 66
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD DAZAP1
[1] 67
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 7.11 0.627 3.55
strata=LOW 4 4 1.89 2.361 3.55
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 1.5219 4.5809 0.8798 1.73 0.0837
Likelihood ratio test=3.23 on 1 df, p=0.07236
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD PEX2
[1] 68
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.07 0.811 1.12
strata=LOW 5 5 5.93 0.146 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 -1.0234 0.3594 1.0080 -1.015 0.31
Likelihood ratio test=0.99 on 1 df, p=0.3196
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD MIR124-3
============================
TCGA-COAD TRIM21
[1] 69
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MEG3
[1] 70
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=10, 12 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 6.35 0.0194 0.0633
strata=LOW 4 4 3.65 0.0337 0.0633
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 0.1795 1.1967 0.7145 0.251 0.802
Likelihood ratio test=0.06 on 1 df, p=0.8017
n= 10, number of events= 10
(12 observations deleted due to missingness)
============================
TCGA-COAD GCLC
[1] 71
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.143 5.143 6
strata=LOW 6 6 6.857 0.107 6
Chisq= 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 -2.201e+01 2.765e-10 2.455e+04 -0.001 0.999
Likelihood ratio test=3.89 on 1 df, p=0.04852
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD IDH2
[1] 72
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 6.38 0.0226 0.0901
strata=LOW 3 3 2.62 0.0550 0.0901
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 0.2316 1.2606 0.7733 0.299 0.765
Likelihood ratio test=0.09 on 1 df, p=0.766
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD FNDC5
[1] 73
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 6.05 0.181 0.947
strata=LOW 3 3 1.95 0.561 0.947
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 0.8766 2.4026 0.9275 0.945 0.345
Likelihood ratio test=0.92 on 1 df, p=0.338
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD FANCD2
[1] 74
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD LCN2
[1] 75
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD TFR2
[1] 76
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4 0.248 0.68
strata=LOW 4 4 3 0.330 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 2.0353 0.8786 0.809 0.419
Likelihood ratio test=0.69 on 1 df, p=0.405
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD PARP12
[1] 77
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.35 0.0528 0.0894
strata=LOW 5 5 4.65 0.0267 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 1.2994 0.8781 0.298 0.766
Likelihood ratio test=0.09 on 1 df, p=0.7626
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD NR1D1
[1] 78
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.017 0.206 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= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD ATG13
[1] 79
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD TMSB4X
[1] 80
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.07 0.811 1.12
strata=LOW 5 5 5.93 0.146 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 -1.0234 0.3594 1.0080 -1.015 0.31
Likelihood ratio test=0.99 on 1 df, p=0.3196
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD CDK14
[1] 81
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.34 0.0263 0.0784
strata=LOW 3 3 2.66 0.0429 0.0784
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 0.2301 1.2588 0.8234 0.279 0.78
Likelihood ratio test=0.08 on 1 df, p=0.7801
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD RP1-228H13.5
[1] 82
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=10, 12 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 7 7 7.88 0.0985 0.506
strata=LOW 3 3 2.12 0.3662 0.506
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 0.5195 1.6811 0.7378 0.704 0.481
Likelihood ratio test=0.47 on 1 df, p=0.4923
n= 10, number of events= 10
(12 observations deleted due to missingness)
============================
TCGA-COAD NOX3
============================
TCGA-COAD IFNA17
============================
TCGA-COAD ALOX12B
[1] 83
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.25 0.300 1.41
strata=LOW 3 3 1.75 0.902 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 2.8527 0.9216 1.137 0.255
Likelihood ratio test=1.33 on 1 df, p=0.2494
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD PGRMC1
[1] 84
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.91 0.619 1.03
strata=LOW 4 4 5.09 0.233 1.03
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 -0.9149 0.4005 0.9283 -0.986 0.324
Likelihood ratio test=1 on 1 df, p=0.3178
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD ULK1
[1] 85
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 6.41 0.311 1.9
strata=LOW 3 3 1.59 1.258 1.9
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 1.2154 3.3716 0.9303 1.306 0.191
Likelihood ratio test=1.74 on 1 df, p=0.1865
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD TRIM26
[1] 86
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD QSOX1
[1] 87
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD ATM
[1] 88
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.5 0.0702 0.172
strata=LOW 4 4 3.5 0.0700 0.172
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 0.3601 1.4335 0.8738 0.412 0.68
Likelihood ratio test=0.18 on 1 df, p=0.6751
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD MIB2
[1] 89
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.63 0.0704 0.281
strata=LOW 3 3 2.37 0.1673 0.281
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 0.4324 1.5409 0.8224 0.526 0.599
Likelihood ratio test=0.27 on 1 df, p=0.6005
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD SLC1A5
[1] 90
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR2115
============================
TCGA-COAD LINC00336
[1] 91
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD NDRG1
[1] 92
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.86 0.00666 0.0131
strata=LOW 4 4 4.14 0.00461 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 0.90969 0.82764 -0.114 0.909
Likelihood ratio test=0.01 on 1 df, p=0.909
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD TAFAZZIN
[1] 93
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR135B
============================
TCGA-COAD GLS2
[1] 94
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD HELLS
[1] 95
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 7.01 0.147 0.732
strata=LOW 3 3 1.99 0.518 0.732
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 0.6472 1.9103 0.7694 0.841 0.4
Likelihood ratio test=0.68 on 1 df, p=0.4108
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD KLF2
[1] 96
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD TFAP2A
[1] 97
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD FURIN
[1] 98
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD CDH1
[1] 99
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD MIR6852
============================
TCGA-COAD MIR670
============================
TCGA-COAD TYRO3
============================
TCGA-COAD MIR4715
============================
TCGA-COAD ABHD12
[1] 100
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=10, 12 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.17 0.00914 0.0155
strata=LOW 7 7 6.83 0.00424 0.0155
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 0.09175 1.09609 0.73796 0.124 0.901
Likelihood ratio test=0.02 on 1 df, p=0.9007
n= 10, number of events= 10
(12 observations deleted due to missingness)
============================
TCGA-COAD ATG7
[1] 101
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.45 0.0880 0.178
strata=LOW 5 5 5.55 0.0547 0.178
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 -0.3253 0.7223 0.7741 -0.42 0.674
Likelihood ratio test=0.18 on 1 df, p=0.6726
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD MT1G
[1] 102
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.95 0.000730 0.00118
strata=LOW 6 6 6.05 0.000357 0.00118
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 -0.02538 0.97494 0.73825 -0.034 0.973
Likelihood ratio test=0 on 1 df, p=0.9726
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD SAT1
[1] 103
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR182
============================
TCGA-COAD HOTAIR
[1] 104
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=10, 24 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.6 0.0436 0.0739
strata=LOW 6 6 6.4 0.0246 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 -0.1837 0.8322 0.6764 -0.272 0.786
Likelihood ratio test=0.07 on 1 df, p=0.7868
n= 10, number of events= 10
(24 observations deleted due to missingness)
============================
TCGA-COAD PIR
[1] 105
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD ELAVL1
[1] 106
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD ACADSB
[1] 107
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD NCOA4
[1] 108
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.6 0.0987 0.147
strata=LOW 5 5 5.4 0.0293 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 0.7044 0.9188 -0.381 0.703
Likelihood ratio test=0.14 on 1 df, p=0.7067
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD IFNA10
============================
TCGA-COAD IFNA13
============================
TCGA-COAD MIR9-2
============================
TCGA-COAD RRM2
[1] 109
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.75 0.120 0.417
strata=LOW 3 3 2.25 0.254 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 1.6977 0.8287 0.639 0.523
Likelihood ratio test=0.4 on 1 df, p=0.5252
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD EPSTI1
[1] 110
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.67 0.0294 0.0643
strata=LOW 4 4 4.33 0.0249 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 0.8210 0.7788 -0.253 0.8
Likelihood ratio test=0.06 on 1 df, p=0.7994
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD LINC00551
[1] 111
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 6.24 0.00927 0.095
strata=LOW 1 1 0.76 0.07614 0.095
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 0.3563 1.4281 1.1621 0.307 0.759
Likelihood ratio test=0.09 on 1 df, p=0.7661
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD SLC25A28
[1] 112
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD LINC00973
============================
TCGA-COAD MIR378A
============================
TCGA-COAD MGST1
[1] 113
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 3.94 0.286 0.693
strata=LOW 3 3 4.06 0.277 0.693
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 -0.7036 0.4948 0.8598 -0.818 0.413
Likelihood ratio test=0.72 on 1 df, p=0.3949
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD MIB1
============================
TCGA-COAD SRC
[1] 114
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD ATG5
[1] 115
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.12 0.365 0.573
strata=LOW 6 6 6.88 0.113 0.573
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 -0.6139 0.5413 0.8233 -0.746 0.456
Likelihood ratio test=0.55 on 1 df, p=0.4592
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD ACVR1B
[1] 116
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD NT5DC2
[1] 117
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD PIK3CA
============================
TCGA-COAD NUPR1
[1] 118
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5 0.198 0.68
strata=LOW 4 4 3 0.330 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 2.0353 0.8786 0.809 0.419
Likelihood ratio test=0.69 on 1 df, p=0.405
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD AKT1S1
[1] 119
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 6.55 0.0456 0.19
strata=LOW 3 3 2.45 0.1217 0.19
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 0.3335 1.3959 0.7691 0.434 0.665
Likelihood ratio test=0.18 on 1 df, p=0.6676
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD MIR19A
============================
TCGA-COAD USP7
[1] 120
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.76 0.101 0.64
strata=LOW 2 2 1.24 0.473 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 2.0636 0.9243 0.784 0.433
Likelihood ratio test=0.58 on 1 df, p=0.4477
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD TMSB4Y
[1] 121
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 20 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
(20 observations deleted due to missingness)
============================
TCGA-COAD SIAH2
[1] 122
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.06 0.001204 0.00227
strata=LOW 5 5 4.94 0.000746 0.00227
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 0.0375 1.0382 0.7869 0.048 0.962
Likelihood ratio test=0 on 1 df, p=0.962
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD MIR29A
============================
TCGA-COAD CHAC1
[1] 123
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD LINC00616
============================
TCGA-COAD PRKAA2
[1] 124
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD LONP1
[1] 125
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 7 7 8.218 0.181 2.39
strata=LOW 2 2 0.782 1.898 2.39
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 1.438 4.213 1.009 1.425 0.154
Likelihood ratio test=1.88 on 1 df, p=0.17
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD PPARG
[1] 126
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.85 0.01176 0.0172
strata=LOW 6 6 6.15 0.00354 0.0172
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 -0.1145 0.8918 0.8720 -0.131 0.896
Likelihood ratio test=0.02 on 1 df, p=0.8962
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD MAPK1
[1] 127
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.36 0.1211 0.239
strata=LOW 4 4 4.64 0.0878 0.239
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 -0.3754 0.6870 0.7728 -0.486 0.627
Likelihood ratio test=0.24 on 1 df, p=0.6251
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD PEX6
[1] 128
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD PPARA
[1] 129
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD ACSL4
[1] 130
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 2.68 2.01 3.9
strata=LOW 3 3 5.32 1.01 3.9
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 -1.945 0.143 1.119 -1.738 0.0823
Likelihood ratio test=4.12 on 1 df, p=0.04246
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD ANO6
[1] 131
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.217 0.0111 0.0824
strata=LOW 1 1 0.783 0.0599 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 0.353 1.423 1.236 0.286 0.775
Likelihood ratio test=0.08 on 1 df, p=0.7797
n= 5, number of events= 5
(17 observations deleted due to missingness)
============================
TCGA-COAD YTHDC2
[1] 132
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(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=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.21 0.00871 0.0279
strata=LOW 3 3 2.79 0.01629 0.0279
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 0.1294 1.1381 0.7754 0.167 0.867
Likelihood ratio test=0.03 on 1 df, p=0.8679
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD PTPN6
[1] 134
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD SMAD7
[1] 135
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.35 0.0528 0.0894
strata=LOW 5 5 4.65 0.0267 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 1.2994 0.8781 0.298 0.766
Likelihood ratio test=0.09 on 1 df, p=0.7626
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD ATG16L1
[1] 136
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD LINC00976
[1] 137
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.48 1.551 2.56
strata=LOW 3 3 4.52 0.509 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 -1.6878 0.1849 1.1718 -1.44 0.15
Likelihood ratio test=2.47 on 1 df, p=0.1159
n= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD H19
[1] 138
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.73 0.0932 0.626
strata=LOW 2 2 1.27 0.4210 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 2.1787 1.0083 0.772 0.44
Likelihood ratio test=0.58 on 1 df, p=0.4453
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD FADS1
[1] 139
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.26 0.0132 0.048
strata=LOW 3 3 2.74 0.0253 0.048
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 0.1816 1.1991 0.8297 0.219 0.827
Likelihood ratio test=0.05 on 1 df, p=0.8269
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD CHP1
[1] 140
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.86 0.00666 0.0131
strata=LOW 4 4 4.14 0.00461 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 0.90969 0.82764 -0.114 0.909
Likelihood ratio test=0.01 on 1 df, p=0.909
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD PRR5
[1] 141
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 6.39 0.302 1.68
strata=LOW 3 3 1.61 1.198 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 1.035 2.816 0.831 1.246 0.213
Likelihood ratio test=1.49 on 1 df, p=0.2217
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD CFL1
[1] 142
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD MIR382
============================
TCGA-COAD LAMP2
[1] 143
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD PTPN14
[1] 144
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 6.93 0.125 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= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD AGPAT3
[1] 145
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD STING1
[1] 146
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.44 0.0435 0.1
strata=LOW 5 5 4.56 0.0424 0.1
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 0.2328 1.2621 0.7364 0.316 0.752
Likelihood ratio test=0.1 on 1 df, p=0.7499
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD ABCC1
[1] 147
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 6.21 0.237 1.3
strata=LOW 3 3 1.79 0.824 1.3
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 1.0113 2.7491 0.9219 1.097 0.273
Likelihood ratio test=1.24 on 1 df, p=0.2664
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD IFNA5
============================
TCGA-COAD MIR140
============================
TCGA-COAD MYB
[1] 148
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD IFNA6
============================
TCGA-COAD IFNA14
============================
TCGA-COAD BDNF-AS
[1] 149
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD TRIB2
[1] 150
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MALAT1
[1] 151
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD FH
[1] 152
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.66 0.0429 0.0784
strata=LOW 4 4 4.34 0.0263 0.0784
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 -0.2301 0.7944 0.8234 -0.279 0.78
Likelihood ratio test=0.08 on 1 df, p=0.7801
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD PEX10
[1] 153
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD SCD
[1] 154
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.76 0.0118 0.0332
strata=LOW 3 3 3.24 0.0173 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 0.8685 0.7745 -0.182 0.856
Likelihood ratio test=0.03 on 1 df, p=0.8552
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD FTL
[1] 155
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.8 0.509 0.98
strata=LOW 4 4 5.2 0.275 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 0.4299 0.8764 -0.963 0.335
Likelihood ratio test=0.99 on 1 df, p=0.3197
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD TSC1
[1] 156
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD BRD3
[1] 157
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD SLC16A1
[1] 158
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR132
============================
TCGA-COAD MIR375
============================
TCGA-COAD MIOX
[1] 159
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD ATXN8OS
============================
TCGA-COAD KLHDC3
[1] 160
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD MICU1
[1] 161
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD CBS
[1] 162
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD HUWE1
[1] 163
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.383 0.0273 0.302
strata=LOW 1 1 0.617 0.2383 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 1.9434 1.2307 0.54 0.589
Likelihood ratio test=0.27 on 1 df, p=0.6049
n= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD LINC00472
[1] 164
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.73 0.0932 0.626
strata=LOW 2 2 1.27 0.4210 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 2.1787 1.0083 0.772 0.44
Likelihood ratio test=0.58 on 1 df, p=0.4453
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD FGF21
============================
TCGA-COAD MIR34A
============================
TCGA-COAD IDH1
[1] 165
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.12 0.365 0.573
strata=LOW 5 5 5.88 0.132 0.573
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 -0.6139 0.5413 0.8233 -0.746 0.456
Likelihood ratio test=0.55 on 1 df, p=0.4592
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD GSK3B
[1] 166
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.18 0.00803 0.03
strata=LOW 2 2 1.82 0.01850 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 1.1739 0.9273 0.173 0.863
Likelihood ratio test=0.03 on 1 df, p=0.8635
n= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD KDM4A
[1] 167
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD PEX12
[1] 168
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.34 0.131 0.301
strata=LOW 3 3 3.66 0.120 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 0.6225 0.8721 -0.543 0.587
Likelihood ratio test=0.31 on 1 df, p=0.5787
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD IDO1
[1] 169
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3 0.334 0.61
strata=LOW 5 5 6 0.167 0.61
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 -0.6025 0.5474 0.7816 -0.771 0.441
Likelihood ratio test=0.6 on 1 df, p=0.4376
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD BCAT2
[1] 170
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD ADAM23
[1] 171
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD PEX3
[1] 172
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD ATP5MC3
[1] 173
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD AQP5
[1] 174
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.55 0.0443 0.105
strata=LOW 4 4 4.45 0.0454 0.105
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 -0.2313 0.7935 0.7162 -0.323 0.747
Likelihood ratio test=0.1 on 1 df, p=0.7469
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD ADAMTS9-AS1
[1] 175
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.73 0.0932 0.626
strata=LOW 2 2 1.27 0.4210 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 2.1787 1.0083 0.772 0.44
Likelihood ratio test=0.58 on 1 df, p=0.4453
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD ACSL3
[1] 176
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD DDR2
[1] 177
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 6.49 0.0371 0.571
strata=LOW 1 1 0.51 0.4721 0.571
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 0.8981 2.4550 1.2285 0.731 0.465
Likelihood ratio test=0.47 on 1 df, p=0.4914
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD TERT
[1] 178
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD IFNA7
============================
TCGA-COAD ECH1
[1] 179
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD CS
[1] 180
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD AMN
[1] 181
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD DUOX2
[1] 182
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MBOAT1
[1] 183
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD RNF113A
[1] 184
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR138-1
============================
TCGA-COAD MIR144
============================
TCGA-COAD P4HB
[1] 185
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR338
============================
TCGA-COAD PTGS2
============================
TCGA-COAD ASAH2
[1] 186
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR522
============================
TCGA-COAD GALNT14
[1] 187
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 3.55 0.592 2.19
strata=LOW 1 1 2.45 0.858 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 1.009e-09 2.083e+04 -0.001 0.999
Likelihood ratio test=3.58 on 1 df, p=0.05836
n= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD KDM4C
[1] 188
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD FXN
[1] 189
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 6.15 0.00354 0.0172
strata=LOW 2 2 1.85 0.01176 0.0172
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 0.1145 1.1213 0.8720 0.131 0.896
Likelihood ratio test=0.02 on 1 df, p=0.8962
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD MEF2C
[1] 190
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD MDM2
[1] 191
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD MAP3K14
[1] 192
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD MDM4
[1] 193
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5 0.198 0.68
strata=LOW 4 4 3 0.330 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 2.0353 0.8786 0.809 0.419
Likelihood ratio test=0.69 on 1 df, p=0.405
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD ASMTL-AS1
[1] 194
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD NEAT1
[1] 195
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD COPZ1
[1] 196
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.65 0.0731 0.102
strata=LOW 6 6 6.35 0.0190 0.102
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 -0.2777 0.7576 0.8717 -0.319 0.75
Likelihood ratio test=0.1 on 1 df, p=0.754
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD PLIN2
[1] 197
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.6 0.0987 0.147
strata=LOW 5 5 5.4 0.0293 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 0.7044 0.9188 -0.381 0.703
Likelihood ratio test=0.14 on 1 df, p=0.7067
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD FADS2
[1] 198
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 6.48 0.0357 0.222
strata=LOW 2 2 1.52 0.1523 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 1.5384 0.9207 0.468 0.64
Likelihood ratio test=0.21 on 1 df, p=0.6456
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD MIR7-1
============================
TCGA-COAD TXN
[1] 199
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR302A
============================
TCGA-COAD EGLN2
[1] 200
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.83 0.142 0.48
strata=LOW 4 4 3.17 0.216 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 1.8317 0.8851 0.684 0.494
Likelihood ratio test=0.49 on 1 df, p=0.483
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD NCOA3
[1] 201
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD SREBF1
[1] 202
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD LINC01134
[1] 203
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD MYCN
[1] 204
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD IFNA4
============================
TCGA-COAD DPEP1
[1] 205
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD VDAC2
[1] 206
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD PCBP2-OT1
[1] 207
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 24 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 3.35 0.546 1.21
strata=LOW 6 6 4.65 0.394 1.21
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 1.140 3.126 1.090 1.045 0.296
Likelihood ratio test=1.39 on 1 df, p=0.238
n= 8, number of events= 8
(24 observations deleted due to missingness)
============================
TCGA-COAD KEAP1
[1] 208
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD RPL8
[1] 209
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD ALOX12
[1] 210
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 3.72 0.442 0.842
strata=LOW 4 4 5.28 0.311 0.842
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 -0.6646 0.5145 0.7370 -0.902 0.367
Likelihood ratio test=0.84 on 1 df, p=0.3583
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD ACSF2
[1] 211
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD KDM5A
[1] 212
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD NRAS
[1] 213
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.91 0.619 1.03
strata=LOW 4 4 5.09 0.233 1.03
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 -0.9149 0.4005 0.9283 -0.986 0.324
Likelihood ratio test=1 on 1 df, p=0.3178
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD MIR30E
============================
TCGA-COAD OGFRP1
[1] 214
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD TF
[1] 215
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.39 0.0287 0.0793
strata=LOW 4 4 3.61 0.0430 0.0793
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 0.2002 1.2216 0.7120 0.281 0.779
Likelihood ratio test=0.08 on 1 df, p=0.7788
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD ETV4
[1] 216
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD PLA2G6
[1] 217
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD POR
[1] 218
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD BRPF1
[1] 219
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.5 0.1021 0.178
strata=LOW 4 4 4.5 0.0566 0.178
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 -0.3466 0.7071 0.8247 -0.42 0.674
Likelihood ratio test=0.18 on 1 df, p=0.675
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD TMBIM4
[1] 220
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD KRAS
[1] 221
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD AHCY
[1] 222
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR34C
============================
TCGA-COAD ATG3
[1] 223
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.6 0.0987 0.147
strata=LOW 5 5 5.4 0.0293 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 0.7044 0.9188 -0.381 0.703
Likelihood ratio test=0.14 on 1 df, p=0.7067
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD MIR30B
============================
TCGA-COAD LYRM1
[1] 224
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD SIRT6
[1] 225
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.35 0.0528 0.0894
strata=LOW 5 5 4.65 0.0267 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 1.2994 0.8781 0.298 0.766
Likelihood ratio test=0.09 on 1 df, p=0.7626
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD KMT2D
[1] 226
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD LPIN1
[1] 227
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.43 0.0734 0.192
strata=LOW 3 3 3.57 0.0911 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 0.7124 0.7767 -0.437 0.662
Likelihood ratio test=0.19 on 1 df, p=0.6607
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD MBOAT2
[1] 228
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD KDM3B
[1] 229
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD ARHGEF26-AS1
[1] 230
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR9-1
============================
TCGA-COAD AIFM2
[1] 231
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD PRDX1
[1] 232
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.16 0.325 0.582
strata=LOW 4 4 4.84 0.145 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 0.5020 0.9205 -0.749 0.454
Likelihood ratio test=0.58 on 1 df, p=0.4481
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD FOXO4
[1] 233
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD BMAL1
[1] 234
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.3 0.0216 0.0544
strata=LOW 4 4 3.7 0.0251 0.0544
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 0.1798 1.1970 0.7718 0.233 0.816
Likelihood ratio test=0.05 on 1 df, p=0.8152
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD MIR127
============================
TCGA-COAD TGFBR1
[1] 235
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 5.91 0.00146 0.0104
strata=LOW 1 1 1.09 0.00789 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 -0.1153 0.8911 1.1325 -0.102 0.919
Likelihood ratio test=0.01 on 1 df, p=0.918
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD NR1D2
[1] 236
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD FZD7
[1] 237
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD G6PD
[1] 238
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD HRAS
[1] 239
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD SLC38A1
[1] 240
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD SLC39A14
[1] 241
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.86 0.00666 0.0131
strata=LOW 4 4 4.14 0.00461 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 0.90969 0.82764 -0.114 0.909
Likelihood ratio test=0.01 on 1 df, p=0.909
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD MIR21
============================
TCGA-COAD MIR1-1
============================
TCGA-COAD PROM2
[1] 242
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 6.44 0.320 1.29
strata=LOW 4 4 2.56 0.803 1.29
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 0.8509 2.3417 0.7710 1.104 0.27
Likelihood ratio test=1.23 on 1 df, p=0.2671
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD NFE2L2
[1] 243
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.12 0.00326 0.00697
strata=LOW 5 5 4.88 0.00275 0.00697
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 0.06012 1.06196 0.72018 0.083 0.933
Likelihood ratio test=0.01 on 1 df, p=0.9335
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD GABARAPL1
[1] 244
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR335
============================
TCGA-COAD PTEN
[1] 245
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3 0.337 0.601
strata=LOW 4 4 5 0.202 0.601
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 -0.5903 0.5542 0.7717 -0.765 0.444
Likelihood ratio test=0.59 on 1 df, p=0.4412
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD PARP4
[1] 246
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.62 0.0550 0.0901
strata=LOW 6 6 6.38 0.0226 0.0901
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 -0.2316 0.7933 0.7733 -0.299 0.765
Likelihood ratio test=0.09 on 1 df, p=0.766
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD MS4A15
[1] 247
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD TIMM9
[1] 248
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD PARP3
[1] 249
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD WIPI1
[1] 250
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD SNX5
[1] 251
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.76 0.07614 0.095
strata=LOW 6 6 6.24 0.00927 0.095
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 -0.3563 0.7003 1.1621 -0.307 0.759
Likelihood ratio test=0.09 on 1 df, p=0.7661
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD LINC00239
[1] 252
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.74 0.0253 0.048
strata=LOW 5 5 5.26 0.0132 0.048
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 -0.1816 0.8339 0.8297 -0.219 0.827
Likelihood ratio test=0.05 on 1 df, p=0.8269
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD PIEZO1
[1] 253
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.017 0.206 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= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD AKR1C2
[1] 254
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR4443
============================
TCGA-COAD SLC16A1-AS1
[1] 255
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 6.08 0.192 0.917
strata=LOW 3 3 1.92 0.607 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 2.1742 0.8298 0.936 0.349
Likelihood ratio test=0.86 on 1 df, p=0.3546
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD FAR1
[1] 256
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD CISD2
[1] 257
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD MAPK3
[1] 258
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD CYGB
[1] 259
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD MLST8
[1] 260
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD PANX2
[1] 261
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD PEBP1
[1] 262
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.91 0.407 0.72
strata=LOW 4 4 5.09 0.233 0.72
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 -0.6498 0.5222 0.7780 -0.835 0.404
Likelihood ratio test=0.71 on 1 df, p=0.4003
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD PARP8
[1] 263
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.49 0.1780 0.24
strata=LOW 6 6 6.51 0.0406 0.24
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 -0.4256 0.6534 0.8743 -0.487 0.626
Likelihood ratio test=0.23 on 1 df, p=0.6351
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD GJA1
============================
TCGA-COAD BAP1
[1] 264
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD MAP3K11
[1] 265
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.83 0.00611 0.0158
strata=LOW 4 4 4.17 0.00708 0.0158
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 -0.0928 0.9114 0.7388 -0.126 0.9
Likelihood ratio test=0.02 on 1 df, p=0.8997
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD TTBK2
[1] 266
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.383 0.0273 0.302
strata=LOW 1 1 0.617 0.2383 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 1.9434 1.2307 0.54 0.589
Likelihood ratio test=0.27 on 1 df, p=0.6049
n= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR214
============================
TCGA-COAD PARP15
[1] 267
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD HDDC3
[1] 268
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.62 0.0550 0.0901
strata=LOW 5 5 5.38 0.0268 0.0901
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 -0.2316 0.7933 0.7733 -0.299 0.765
Likelihood ratio test=0.09 on 1 df, p=0.766
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD MIR10A
============================
TCGA-COAD CGAS
[1] 269
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD SIRT2
[1] 270
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD PPARD
[1] 271
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.35 0.0528 0.0894
strata=LOW 5 5 4.65 0.0267 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 1.2994 0.8781 0.298 0.766
Likelihood ratio test=0.09 on 1 df, p=0.7626
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD EGR1
[1] 272
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD AQP3
[1] 273
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD HSF1
[1] 274
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 19 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
(19 observations deleted due to missingness)
============================
TCGA-COAD MIR18A
============================
TCGA-COAD OSBPL9
[1] 275
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 0.902 1.335 1.74
strata=LOW 5 5 6.098 0.198 1.74
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 -1.2525 0.2858 1.0088 -1.242 0.214
Likelihood ratio test=1.45 on 1 df, p=0.2278
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD SESN2
[1] 276
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD BECN1
[1] 277
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=11, 11 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.01 4.11e-05 7.58e-05
strata=LOW 7 7 6.99 2.36e-05 7.58e-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 0.005905 1.005923 0.678206 0.009 0.993
Likelihood ratio test=0 on 1 df, p=0.9931
n= 11, number of events= 11
(11 observations deleted due to missingness)
============================
TCGA-COAD FTMT
============================
TCGA-COAD HCAR1
[1] 278
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD HILPDA
[1] 279
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.21 0.00871 0.0279
strata=LOW 3 3 2.79 0.01629 0.0279
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 0.1294 1.1381 0.7754 0.167 0.867
Likelihood ratio test=0.03 on 1 df, p=0.8679
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD GSTM1
[1] 280
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD MIR222
============================
TCGA-COAD RARRES2
[1] 281
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD BRD4
[1] 282
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD SOCS1
[1] 283
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.5 0.0566 0.178
strata=LOW 3 3 2.5 0.1021 0.178
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 0.3466 1.4142 0.8247 0.42 0.674
Likelihood ratio test=0.18 on 1 df, p=0.675
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD MIR17
============================
TCGA-COAD GDF15
[1] 284
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD ARF6
[1] 285
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 4.24 0.361 0.904
strata=LOW 5 5 3.76 0.407 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 2.1947 0.8464 0.929 0.353
Likelihood ratio test=0.94 on 1 df, p=0.3319
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD CDO1
[1] 286
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD CAMKK2
[1] 287
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD LINC01606
[1] 288
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=11, 27 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.84 0.184 0.321
strata=LOW 8 8 7.16 0.099 0.321
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 0.4022 1.4952 0.7137 0.564 0.573
Likelihood ratio test=0.33 on 1 df, p=0.5645
n= 11, number of events= 11
(27 observations deleted due to missingness)
============================
TCGA-COAD BACH1
[1] 289
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.5 0.893 1.85
strata=LOW 3 3 4.5 0.497 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 -1.4295 0.2394 1.1334 -1.261 0.207
Likelihood ratio test=1.98 on 1 df, p=0.159
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD DPP4
[1] 290
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 5.32 1.01 3.9
strata=LOW 5 5 2.68 2.01 3.9
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 1.945 6.995 1.119 1.738 0.0823
Likelihood ratio test=4.12 on 1 df, p=0.04246
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD PPP1R13L
[1] 291
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.35 0.0965 0.22
strata=LOW 4 4 4.65 0.0903 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 0.7065 0.7444 -0.467 0.641
Likelihood ratio test=0.22 on 1 df, p=0.6368
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD MIR150
============================
TCGA-COAD FLT3
[1] 292
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 1.09 0.00789 0.0104
strata=LOW 6 6 5.91 0.00146 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 0.1153 1.1222 1.1325 0.102 0.919
Likelihood ratio test=0.01 on 1 df, p=0.918
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD MAP1LC3A
[1] 293
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.93 0.388 0.961
strata=LOW 2 2 3.07 0.371 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 -1.0569 0.3475 1.1267 -0.938 0.348
Likelihood ratio test=1.05 on 1 df, p=0.3051
n= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD A2M-AS1
[1] 294
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD PDSS2
[1] 295
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.86 0.00666 0.0131
strata=LOW 4 4 4.14 0.00461 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 0.90969 0.82764 -0.114 0.909
Likelihood ratio test=0.01 on 1 df, p=0.909
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD DNAJB6
[1] 296
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD SUV39H1
[1] 297
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.017 0.206 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= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD LPCAT3
[1] 298
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD MIR761
============================
TCGA-COAD CDCA3
[1] 299
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD EPAS1
[1] 300
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.89 0.00251 0.00877
strata=LOW 3 3 3.11 0.00394 0.00877
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 -0.08043 0.92272 0.85887 -0.094 0.925
Likelihood ratio test=0.01 on 1 df, p=0.925
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD SLC11A2
[1] 301
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.67 0.661 1.5
strata=LOW 3 3 4.33 0.408 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 -1.3134 0.2689 1.1415 -1.151 0.25
Likelihood ratio test=1.62 on 1 df, p=0.2028
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD CREB3
[1] 302
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD ATF3
[1] 303
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.73 0.197 0.559
strata=LOW 3 3 2.27 0.237 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 2.3292 1.1634 0.727 0.467
Likelihood ratio test=0.59 on 1 df, p=0.4413
n= 5, number of events= 5
(17 observations deleted due to missingness)
============================
TCGA-COAD TGFB1
[1] 304
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 2.93 1.463 2.97
strata=LOW 3 3 5.07 0.845 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 -1.7133 0.1803 1.1083 -1.546 0.122
Likelihood ratio test=3.22 on 1 df, p=0.07281
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD SMG9
[1] 305
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=10, 12 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 7.54 0.316 1.46
strata=LOW 4 4 2.46 0.972 1.46
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 0.8533 2.3475 0.7250 1.177 0.239
Likelihood ratio test=1.35 on 1 df, p=0.245
n= 10, number of events= 10
(12 observations deleted due to missingness)
============================
TCGA-COAD NOX4
[1] 306
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.73 0.0932 0.626
strata=LOW 2 2 1.27 0.4210 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 2.1787 1.0083 0.772 0.44
Likelihood ratio test=0.58 on 1 df, p=0.4453
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD MIR27A
============================
TCGA-COAD FOXP1
[1] 307
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD SNCA
[1] 308
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD ENPP2
[1] 309
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.48 1.551 2.56
strata=LOW 3 3 4.52 0.509 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 -1.6878 0.1849 1.1718 -1.44 0.15
Likelihood ratio test=2.47 on 1 df, p=0.1159
n= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD BRD2
[1] 310
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.5 0.893 1.85
strata=LOW 3 3 4.5 0.497 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 -1.4295 0.2394 1.1334 -1.261 0.207
Likelihood ratio test=1.98 on 1 df, p=0.159
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD ISCU
[1] 311
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD PHF21A
[1] 312
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.73 0.0932 0.626
strata=LOW 2 2 1.27 0.4210 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 2.1787 1.0083 0.772 0.44
Likelihood ratio test=0.58 on 1 df, p=0.4453
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD PARP6
[1] 313
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD ZEB1
[1] 314
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.73 0.0932 0.626
strata=LOW 2 2 1.27 0.4210 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 2.1787 1.0083 0.772 0.44
Likelihood ratio test=0.58 on 1 df, p=0.4453
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD LIG3
[1] 315
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD PEDS1
[1] 316
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.6 0.0638 0.359
strata=LOW 2 2 1.4 0.2547 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 1.7238 0.9202 0.592 0.554
Likelihood ratio test=0.33 on 1 df, p=0.5629
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD RPPH1
============================
TCGA-COAD GFRA1
[1] 317
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.217 0.0111 0.0824
strata=LOW 1 1 0.783 0.0599 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 0.353 1.423 1.236 0.286 0.775
Likelihood ratio test=0.08 on 1 df, p=0.7797
n= 5, number of events= 5
(17 observations deleted due to missingness)
============================
TCGA-COAD AQP8
[1] 318
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 2.6 0.1394 0.23
strata=LOW 6 6 5.4 0.0672 0.23
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 0.4055 1.5000 0.8503 0.477 0.633
Likelihood ratio test=0.24 on 1 df, p=0.625
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD SIRT1
[1] 319
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR15A
============================
TCGA-COAD AKR1C3
[1] 320
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD DLD
[1] 321
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD USP11
[1] 322
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.72 0.606 2.01
strata=LOW 1 1 2.28 0.721 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 9.533e-10 2.244e+04 -0.001 0.999
Likelihood ratio test=3.22 on 1 df, p=0.07279
n= 5, number of events= 5
(17 observations deleted due to missingness)
============================
TCGA-COAD SREBF2
[1] 323
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD MIR190A
============================
TCGA-COAD IFNA8
============================
TCGA-COAD KDM6B
[1] 324
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD ACOT1
[1] 325
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD RELA
[1] 326
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD SLC39A7
[1] 327
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD POM121L12
============================
TCGA-COAD MIR101-1
============================
TCGA-COAD GABPB1-AS1
[1] 328
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.83 0.179 0.48
strata=LOW 4 4 3.17 0.216 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 1.8317 0.8851 0.684 0.494
Likelihood ratio test=0.49 on 1 df, p=0.483
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD EGFR
[1] 329
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD BRD7
[1] 330
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD MIR1287
============================
TCGA-COAD MIR23A
============================
TCGA-COAD LCE2C
============================
TCGA-COAD ADAMTS13
[1] 331
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD SIRT3
[1] 332
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD CIRBP
[1] 333
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD BRDT
============================
TCGA-COAD KIF4A
[1] 334
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD CPEB1
[1] 335
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 6.48 0.0357 0.222
strata=LOW 2 2 1.52 0.1523 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 1.5384 0.9207 0.468 0.64
Likelihood ratio test=0.21 on 1 df, p=0.6456
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD LINC01833
[1] 336
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 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
(20 observations deleted due to missingness)
============================
TCGA-COAD MAPKAP1
[1] 337
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD ATF4
[1] 338
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD SLC7A11
[1] 339
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 6.39 0.302 1.68
strata=LOW 3 3 1.61 1.198 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 1.035 2.816 0.831 1.246 0.213
Likelihood ratio test=1.49 on 1 df, p=0.2217
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD EMC2
[1] 340
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD WWTR1
[1] 341
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.73 0.0932 0.626
strata=LOW 2 2 1.27 0.4210 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 2.1787 1.0083 0.772 0.44
Likelihood ratio test=0.58 on 1 df, p=0.4453
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD HSPA5
[1] 342
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD BEX1
[1] 343
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.76 0.0118 0.0332
strata=LOW 3 3 3.24 0.0173 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 0.8685 0.7745 -0.182 0.856
Likelihood ratio test=0.03 on 1 df, p=0.8552
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD PML
[1] 344
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 5.91 0.00146 0.0104
strata=LOW 1 1 1.09 0.00789 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 -0.1153 0.8911 1.1325 -0.102 0.919
Likelihood ratio test=0.01 on 1 df, p=0.918
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD MIR142
============================
TCGA-COAD AEBP2
[1] 345
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD GPAT4
[1] 346
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD CA9
[1] 347
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.383 0.0273 0.302
strata=LOW 1 1 0.617 0.2383 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 1.9434 1.2307 0.54 0.589
Likelihood ratio test=0.27 on 1 df, p=0.6049
n= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD STK11
[1] 348
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 7.51 0.305 2.08
strata=LOW 3 3 1.49 1.543 2.08
Chisq= 2.1 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 1.1333 3.1060 0.8255 1.373 0.17
Likelihood ratio test=1.8 on 1 df, p=0.18
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD TBK1
[1] 349
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD CDKN2A
[1] 350
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=3, 19 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.833 0.0333 0.0588
strata=LOW 2 2 2.167 0.0128 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 0.7071 1.4355 -0.241 0.809
Likelihood ratio test=0.06 on 1 df, p=0.8096
n= 3, number of events= 3
(19 observations deleted due to missingness)
============================
TCGA-COAD DCAF7
[1] 351
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD MTF1
[1] 352
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD MEG8
[1] 353
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.55 0.0443 0.105
strata=LOW 4 4 4.45 0.0454 0.105
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 -0.2313 0.7935 0.7162 -0.323 0.747
Likelihood ratio test=0.1 on 1 df, p=0.7469
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD CLTRN
[1] 354
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD PARP11
[1] 355
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 5.3 0.0935 0.259
strata=LOW 3 3 3.7 0.1337 0.259
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 -0.3766 0.6862 0.7445 -0.506 0.613
Likelihood ratio test=0.26 on 1 df, p=0.6085
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD GABARAPL2
[1] 356
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.07 0.811 1.12
strata=LOW 5 5 5.93 0.146 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 -1.0234 0.3594 1.0080 -1.015 0.31
Likelihood ratio test=0.99 on 1 df, p=0.3196
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD CDKN1A
[1] 357
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.65 0.0731 0.102
strata=LOW 6 6 6.35 0.0190 0.102
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 -0.2777 0.7576 0.8717 -0.319 0.75
Likelihood ratio test=0.1 on 1 df, p=0.754
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD NEDD4L
[1] 358
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD AR
[1] 359
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.383 0.0273 0.302
strata=LOW 1 1 0.617 0.2383 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 1.9434 1.2307 0.54 0.589
Likelihood ratio test=0.27 on 1 df, p=0.6049
n= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR20A
============================
TCGA-COAD HMOX1
[1] 360
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 3.07 0.001607 0.00297
strata=LOW 6 6 5.93 0.000832 0.00297
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 0.04233 1.04324 0.77735 0.054 0.957
Likelihood ratio test=0 on 1 df, p=0.9565
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD ZFP36
[1] 361
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD MIR744
============================
TCGA-COAD CTSB
[1] 362
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 1.91 2.281 3.81
strata=LOW 4 4 6.09 0.716 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 -1.9249 0.1459 1.1313 -1.702 0.0888
Likelihood ratio test=3.77 on 1 df, p=0.05213
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD AGPS
[1] 363
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD MT1DP
[1] 364
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=11, 11 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 6.03 0.177 0.463
strata=LOW 6 6 4.97 0.215 0.463
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 0.4356 1.5460 0.6450 0.675 0.499
Likelihood ratio test=0.45 on 1 df, p=0.5009
n= 11, number of events= 11
(11 observations deleted due to missingness)
============================
TCGA-COAD SNX4
[1] 365
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 2 2 1.49 0.1780 0.24
strata=LOW 6 6 6.51 0.0406 0.24
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 -0.4256 0.6534 0.8743 -0.487 0.626
Likelihood ratio test=0.23 on 1 df, p=0.6351
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD NR4A1
[1] 366
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MFN2
[1] 367
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=10, 12 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 7 7 8.61 0.30 2.48
strata=LOW 3 3 1.39 1.85 2.48
Chisq= 2.5 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 1.2377 3.4478 0.8322 1.487 0.137
Likelihood ratio test=2.1 on 1 df, p=0.1477
n= 10, number of events= 10
(12 observations deleted due to missingness)
============================
TCGA-COAD SELENOI
[1] 368
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD AGAP2-AS1
[1] 369
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD TRIM46
[1] 370
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.55 0.0443 0.105
strata=LOW 4 4 4.45 0.0454 0.105
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 -0.2313 0.7935 0.7162 -0.323 0.747
Likelihood ratio test=0.1 on 1 df, p=0.7469
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD CYB5R1
[1] 371
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.93 0.00152 0.00462
strata=LOW 2 2 2.07 0.00215 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 0.93310 1.01903 -0.068 0.946
Likelihood ratio test=0 on 1 df, p=0.9458
n= 5, number of events= 5
(17 observations deleted due to missingness)
============================
TCGA-COAD PARK7
[1] 372
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD CARS1
[1] 373
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD NOX1
[1] 374
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD VDR
[1] 375
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.95 0.642 2.97
strata=LOW 4 4 2.05 1.868 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 4.1439 0.8862 1.604 0.109
Likelihood ratio test=2.77 on 1 df, p=0.0958
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD PROK2
[1] 376
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 2.5 0.893 1.85
strata=LOW 3 3 4.5 0.497 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 -1.4295 0.2394 1.1334 -1.261 0.207
Likelihood ratio test=1.98 on 1 df, p=0.159
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD FABP4
[1] 377
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD ABCB10
[1] 378
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD CP
[1] 379
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD MIR4735
============================
TCGA-COAD MIR130A
============================
TCGA-COAD TUG1
[1] 380
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.383 0.0273 0.302
strata=LOW 1 1 0.617 0.2383 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 1.9434 1.2307 0.54 0.589
Likelihood ratio test=0.27 on 1 df, p=0.6049
n= 6, number of events= 6
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR9-3HG
[1] 381
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 1.79 0.824 1.3
strata=LOW 5 5 6.21 0.237 1.3
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 -1.0113 0.3638 0.9219 -1.097 0.273
Likelihood ratio test=1.24 on 1 df, p=0.2664
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD MIR196C
============================
TCGA-COAD IFNA21
============================
TCGA-COAD RP11-274B21.9
[1] 382
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4 5.68e-06 1.35e-05
strata=LOW 4 4 4 5.66e-06 1.35e-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 -0.002835 0.997169 0.771518 -0.004 0.997
Likelihood ratio test=0 on 1 df, p=0.9971
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD PVT1
[1] 383
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.64 0.0878 0.337
strata=LOW 3 3 2.36 0.1724 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 1.7037 0.9273 0.575 0.566
Likelihood ratio test=0.34 on 1 df, p=0.5611
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD MIR539
============================
TCGA-COAD IFNA2
============================
TCGA-COAD TFRC
[1] 384
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD ALOX15B
[1] 385
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 1.59 0.221 0.325
strata=LOW 6 6 5.41 0.065 0.325
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 0.6349 1.8869 1.1293 0.562 0.574
Likelihood ratio test=0.36 on 1 df, p=0.5505
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD MPC1
[1] 386
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MTCH1
[1] 387
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.34 0.131 0.301
strata=LOW 3 3 3.66 0.120 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 0.6225 0.8721 -0.543 0.587
Likelihood ratio test=0.31 on 1 df, p=0.5787
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD MIR324
============================
TCGA-COAD SNHG14
[1] 388
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 6.15 0.00354 0.0172
strata=LOW 2 2 1.85 0.01176 0.0172
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 0.1145 1.1213 0.8720 0.131 0.896
Likelihood ratio test=0.02 on 1 df, p=0.8962
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD PDK4
[1] 389
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD DUOX1
[1] 390
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.75 0.098 0.331
strata=LOW 4 4 3.25 0.173 0.331
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 0.4407 1.5539 0.7721 0.571 0.568
Likelihood ratio test=0.33 on 1 df, p=0.5656
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD LINC00886
[1] 391
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD NF2
[1] 392
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 8 8 8.764 0.0666 2.8
strata=LOW 1 1 0.236 2.4714 2.8
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 2.013 7.483 1.415 1.422 0.155
Likelihood ratio test=1.75 on 1 df, p=0.1855
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD MIR149
============================
TCGA-COAD CYP4F8
[1] 393
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 6.94 0.545 2.71
strata=LOW 4 4 2.06 1.840 2.71
Chisq= 2.7 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 1.2216 3.3925 0.7824 1.561 0.118
Likelihood ratio test=2.44 on 1 df, p=0.1185
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD AKR1C1
[1] 394
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD PRKCA
[1] 395
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD CD44
[1] 396
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.8 0.0100 0.0262
strata=LOW 3 3 3.2 0.0119 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 0.8749 0.8268 -0.162 0.872
Likelihood ratio test=0.03 on 1 df, p=0.8716
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD FBXW7
[1] 397
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD YAP1
[1] 398
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MTOR
[1] 399
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD RICTOR
[1] 400
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 3.55 0.0558 0.142
strata=LOW 3 3 3.45 0.0575 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 0.7298 0.8385 -0.376 0.707
Likelihood ratio test=0.14 on 1 df, p=0.7076
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD WIPI2
[1] 401
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD IREB2
[1] 402
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.37 0.1673 0.281
strata=LOW 5 5 5.63 0.0704 0.281
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 -0.4324 0.6490 0.8224 -0.526 0.599
Likelihood ratio test=0.27 on 1 df, p=0.6005
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD GOT1
[1] 403
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD CD82
============================
TCGA-COAD MAPK9
[1] 404
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 2.48 0.1102 0.175
strata=LOW 5 5 5.52 0.0495 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 0.7243 0.7740 -0.417 0.677
Likelihood ratio test=0.17 on 1 df, p=0.6797
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD LGMN
[1] 405
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD PARP2
[1] 406
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD MIR16-1
============================
TCGA-COAD ATG4D
[1] 407
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD RBMS1
[1] 408
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 6 6 5.43 0.0599 0.17
strata=LOW 3 3 3.57 0.0911 0.17
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 -0.3047 0.7374 0.7417 -0.411 0.681
Likelihood ratio test=0.17 on 1 df, p=0.6781
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD GSTZ1
[1] 409
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD SRSF9
[1] 410
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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 4 4 4.83 0.142 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= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD HIF1A
[1] 411
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD FNDC3B
[1] 412
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.25 0.300 0.974
strata=LOW 4 4 2.75 0.574 0.974
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 0.7504 2.1178 0.7767 0.966 0.334
Likelihood ratio test=0.95 on 1 df, p=0.3309
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD RHEBP1
============================
TCGA-COAD PSEN1
[1] 413
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.12 0.00326 0.00697
strata=LOW 5 5 4.88 0.00275 0.00697
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 0.06012 1.06196 0.72018 0.083 0.933
Likelihood ratio test=0.01 on 1 df, p=0.9335
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD ADIPOQ
[1] 414
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 5.45 0.388 1.38
strata=LOW 4 4 2.55 0.831 1.38
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 0.8971 2.4525 0.7863 1.141 0.254
Likelihood ratio test=1.32 on 1 df, p=0.2513
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD MUC1
[1] 415
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 6.44 0.320 1.29
strata=LOW 4 4 2.56 0.803 1.29
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 0.8509 2.3417 0.7710 1.104 0.27
Likelihood ratio test=1.23 on 1 df, p=0.2671
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD CAV1
[1] 416
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.73 0.0932 0.626
strata=LOW 2 2 1.27 0.4210 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 2.1787 1.0083 0.772 0.44
Likelihood ratio test=0.58 on 1 df, p=0.4453
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD SEC24B
[1] 417
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=9, 13 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.56 0.0565 0.163
strata=LOW 4 4 3.44 0.0913 0.163
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 0.2872 1.3327 0.7136 0.402 0.687
Likelihood ratio test=0.16 on 1 df, p=0.6879
n= 9, number of events= 9
(13 observations deleted due to missingness)
============================
TCGA-COAD PRDX6
[1] 418
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 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
(14 observations deleted due to missingness)
============================
TCGA-COAD TMEM161B-DT
[1] 419
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD PGD
[1] 420
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 4 4 4.75 0.120 0.417
strata=LOW 3 3 2.25 0.254 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 1.6977 0.8287 0.639 0.523
Likelihood ratio test=0.4 on 1 df, p=0.5252
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD RHOT1
[1] 421
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=4, 18 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
(18 observations deleted due to missingness)
============================
TCGA-COAD ACSL1
[1] 422
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 5.26 0.0132 0.048
strata=LOW 3 3 2.74 0.0253 0.048
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 0.1816 1.1991 0.8297 0.219 0.827
Likelihood ratio test=0.05 on 1 df, p=0.8269
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD NEDD4
[1] 423
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD ELOVL5
[1] 424
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 4.76 0.0118 0.0332
strata=LOW 3 3 3.24 0.0173 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 0.8685 0.7745 -0.182 0.856
Likelihood ratio test=0.03 on 1 df, p=0.8552
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD YY1AP1
[1] 425
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
Display the results only for genes where a significant difference in survival has been reported.
significant_genes [1] "GCLC" "TRIM26" "SLC1A5" "SRC" "TMSB4Y" "ACSL4" "CBS" "ETV4" "SLC38A1" "AKR1C2" "PARP15" "HCAR1" "DPP4"
[14] "CDCA3" "GPAT4" "TBK1" "MTF1" "CLTRN" "LINC00886"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 GCLC Warning: Loglik converged before variable 1 ; coefficient may be infinite. Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 1 1 0.143 5.143 6
strata=LOW 6 6 6.857 0.107 6
Chisq= 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 -2.201e+01 2.765e-10 2.455e+04 -0.001 0.999
Likelihood ratio test=3.89 on 1 df, p=0.04852
n= 7, number of events= 7
(15 observations deleted due to missingness)
============================
TCGA-COAD TRIM26
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD SLC1A5
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD SRC
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD TMSB4Y
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 20 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
(20 observations deleted due to missingness)
============================
TCGA-COAD ACSL4
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 5 5 2.68 2.01 3.9
strata=LOW 3 3 5.32 1.01 3.9
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 -1.945 0.143 1.119 -1.738 0.0823
Likelihood ratio test=4.12 on 1 df, p=0.04246
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD CBS
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD ETV4
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD SLC38A1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD AKR1C2
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD PARP15
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD HCAR1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=7, 15 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
(15 observations deleted due to missingness)
============================
TCGA-COAD DPP4
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=8, 14 observations deleted due to missingness.
N Observed Expected (O-E)^2/E (O-E)^2/V
strata=HIGH 3 3 5.32 1.01 3.9
strata=LOW 5 5 2.68 2.01 3.9
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 1.945 6.995 1.119 1.738 0.0823
Likelihood ratio test=4.12 on 1 df, p=0.04246
n= 8, number of events= 8
(14 observations deleted due to missingness)
============================
TCGA-COAD CDCA3
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD GPAT4
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD TBK1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD MTF1
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=5, 17 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
(17 observations deleted due to missingness)
============================
TCGA-COAD CLTRN
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 observations deleted due to missingness)
============================
TCGA-COAD LINC00886
Call:
survdiff(formula = Surv(overall_survival, deceased) ~ strata,
data = gene_df)
n=6, 16 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
(16 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 Normal 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 == "normal")))

  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

Our genes of interest are the differentially expressed genes.

```{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")
  } 
}
```