Gene Expression Profile Data and Clinical Parameters

The transcriptome of RNA-seq data and clinical parameters of CRC cases (normal samples, 41 cases; tumor samples, 473 cases) were downloaded from The Cancer Genome Atlas Program (TCGA) repository of the National Cancer Institute (https://cancergenome.nih.gov/). The data parameters were as follows: primary site (colon), data category with transcriptome profiling with gene expression and quantification with FPKM and counts, experimental strategy with RNA-Seq analysis and workflow type with HTSeq-FPKM and HTSeq-Counts. Default settings were used for the other filters.

In order to test and verify the discovery in the TCGA cohort, we downloaded {"type":"entrez-geo","attrs":{"text":"GSE14333","term_id":"14333"}}GSE14333 and {"type":"entrez-geo","attrs":{"text":"GSE38832","term_id":"38832"}}GSE38832 from the Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/). Expression series matrix files of both datasets were based on {"type":"entrez-geo","attrs":{"text":"GPL570","term_id":"570"}}GPL570. The former included 290 samples of primary colorectal cancer patients, while the latter had expression data of 122 human samples. To get a larger size of samples, two cohorts were combined for analyses.