Analysis code for: Beyond compound ranking, the HDAC-inhibitor class is the reproducible butyrate-mimicking axis in nasopharyngeal carcinoma cells, with replication in independent pharmacogenomic panels

Abstract

Project name: NPC-butyrate-response-signature, version 1.0.0, released under the MIT licence. Analysis code, software environment and file manifests for the manuscript "Beyond compound ranking: the HDAC-inhibitor class is the reproducible butyrate-mimicking axis in nasopharyngeal carcinoma cells, with replication in independent pharmacogenomic panels" (Research article submitted to Journal of Translational Medicine). The archive holds the complete R and Python pipeline: construction of the two-armed butyrate-response signature from an in-house butyrate RNA-seq experiment in C666-1 and 5-8F cells; hypergeometric enrichment and offline LINCS gene expression signature search (GESS) connectivity mapping against the mirrored L1000 reference library; class-level enrichment across five queries; an evidence- and size-matched null model with 20,000 draws; drug-sensitivity testing in CCLE 2019 and GDSC2; and the figure, table and manuscript-build scripts. MANIFEST_scripts.csv, MANIFEST_tables.csv, MANIFEST_seeds.csv, MANIFEST_env.csv and MANIFEST_summary.csv list every script and intermediate result table with size, modification time and SHA256 (first 16 hex). ENVIRONMENT.txt records the software versions: R 4.5.2 and Python 3.14.7 on Windows 10, with signatureSearch 1.24.0, signatureSearchData 1.24.0, ExperimentHub 3.0.0, rhdf5 2.54.1 and the other packages used. The in-house RNA-seq reads are deposited in the NCBI Sequence Read Archive under BioProject PRJNA1538131 (SRA study SRP741880). The large public reference libraries are not redistributed; REFERENCES_AND_LARGE_FILES.md gives their md5 checksums and retrieval route. The derived result tables are distributed with the article as additional files. The author list follows the current manuscript; the corresponding author confirms the final author order at publication.