4.1. Colon Cancer Dataset and Preprocessing

The workflow of our study is shown in Figure S1A. Public gene-expression data and full clinical annotation were searched for in the GEO and TCGA databases. Patients without survival information were removed from further evaluation. For microarray data from Affymetrix^®, we applied the “limma” package in R for the analysis. As to datasets in TCGA, RNA sequencing data (FPKM value) of gene expression were downloaded from the Genomic Data Commons (GDC, https://portal.gdc.cancer.gov/ (accessed on 8 June 2020)). The somatic mutation data were acquired from the TCGA database. Data were analyzed with the R (version 3.6.2, 2019-12-12) software and R Bioconductor packages.