Analysis code for: Exercise imprints a persistent tumor intrinsic suppressive state in colorectal cancer
Year: 2026
Type: software
Abstract: Analysis code supporting the manuscript "Exercise imprints a persistent tumor intrinsic suppressive state in colorectal cancer". This deposit contains the R code and command histories used for two analyses reported in the paper. 1. Independent re-analysis of the human colorectal cancer survival data. The Kaplan-Meier curves shown in the paper were generated on the R2 platform (http://r2.amc.nl). To obtain hazard ratios with confidence intervals and to make the analysis reproducible from primary data, every panel was re-analysed in R from the original public repositories (GEO accessions GSE24551, GSE39582, GSE72970 and GSE106584; ArrayExpress accession E-MTAB-12862; and the TCGA-COAD Agilent dataset obtained through UCSC Xena), applying the same expression cutoff mode used on the platform. The code derives per-cohort hazard ratios by Cox proportional-hazards regression, compares groups by the log-rank test, checks the proportional-hazards assumption, and combines cohorts by fixed-effect inverse-variance meta-analysis on the log hazard-ratio scale. 2. Command history for the untargeted metabolomic analysis performed in MetaboAnalyst 6.0, documenting the filtering, normalisation and statistical parameters reported in the STAR Methods. Because absolute expression cutoffs are not transferable between preprocessing pipelines, quantile cutoffs were used; these are invariant under monotonic rescaling and therefore reproduce the same dichotomisation as the source platform. Software: R 4.6.1 with the packages survival, dplyr, tidyr, openxlsx, readxl, ggplot2, scales, GEOquery and Biobase.
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7203892814
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