The Cancer Genome Atlas (TCGA) data (TCGA-COAD and TCGA-READ datasets) and NCBI GEO (GSE190826 dataset) were used to examine the expression of SPP1, S100A4 and SPARC and to perform survival analysis in colorectal cancer patients. TCGA data included information about SPP1, S100A4 and SPARC expression, that was evaluated in the following groups of patients: a) with colorectal cancer (common group) (N=417), b) with colon cancer, including transverse colon, ascending colon, descending colon, sigmoid colon, cecum, hepatic flexure, splenic flexure (n=305), c) with rectal cancer, including rectosigmoid junction and rectum (N=112), with available clinical information and records on recurrence and survival rates (in details in Supplementary Table S1). Patients with advanced stage IV were excluded. GSE190826 dataset included 92 patients with rectal cancer treated with neoadjuvant chemoradiotherapy (NCRT); information about pre-treatment levels of SPP1, S100A4 and SPARC mRNA expression was obtained. The TCGA biolinks was used for retrieving RNA-seq data from the GDC database. The raw sequencing reads were processed via the DESeq2 R package. The raw counts were depth normalized and variance stabilized via the variance stabilizing transformation (VST) for downstream survival analysis.
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