Analysis code for: SLC7A11 expression is associated with prognosis and copy-number-defined malignant hepatocytes in hepatocellular carcinoma: an integrative computational analysis

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Analysis code for the manuscript: "SLC7A11 expression is associated with prognosis and copy-number-defined malignant hepatocytes in hepatocellular carcinoma: an integrative computational analysis" — Qiu N., Zhang Y., Pang X., Wu J. This deposit contains the scripts for every analysis reported in the paper, together with a table in README.md mapping each numerical claim in the manuscript to the script that produces it. Version 4 corrects two implementation errors in the non-proportional-hazards survival analysis that were present in version 3 and were identified during peer review: - The early piecewise Cox model was fitted only on patients whose observed follow-up was shorter than two years, which selects the sample on its own outcome. All patients now enter the early interval, with those still under observation at two years censored administratively at that point.- The time-varying covariate was built as z x log(min(t_i, b)), so within a single risk set its value depended on each subject's own event time. The counting-process dataset is now split at every distinct event time, so that every patient at risk at a given time carries the same log(t). Every survival estimate downstream of those models changed: the early hazard ratio moved from 1.54 to 1.49 unadjusted (1.44 adjusted for stage, age and sex), and the log-time interaction from 0.56 to 0.86. The direction of the finding is unchanged; its magnitude was overstated in version 3. The superseded script is retained under revision/obsolete/ as a record of thecorrection and exits immediately if executed. Versions 1-3 cannot reproduce the current manuscript. Scripts resolve all paths relative to the repository root and can be run from any working directory. The input datasets (TCGA-LIHC, ICGC LIRI-JP, GEO GSE14520 and GSE149614, PDB 7CCS, GDSC2) are public and are not redistributed here; README.md lists the sources and CODE_README.md documents the layout,path handling and software environments. An AI assistant (Claude, Anthropic) was used to implement analysis code and prepare figures. All results were reviewed and verified by the authors, who take responsibility for the integrity and accuracy of the work.

Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.