Code and processed data for: A Dry-Lab Framework Linking Cross-Cancer Multi-Omics Prioritization, Genome-Scale Metabolic Rerouting, and Structure-Based Evaluation in Endocrine-Relevant Cancers

This Zenodo record contains the scripts, processed result tables, supplementary benchmark datasets, environment snapshots, and terminal logs supporting the manuscript:

“A Dry-Lab Framework Linking Cross-Cancer Multi-Omics Prioritization, Genome-Scale Metabolic Rerouting, and Structure-Based Evaluation in Endocrine-Relevant Cancers”.

The study was designed as a dry-lab framework integrating public multi-omics datasets, genome-scale metabolic modeling, external validation, LINCS-based perturbational support, and downstream structure-based evaluation in endocrine-relevant cancers, with prostate adenocarcinoma (PRAD) as the primary disease context and breast cancer (BRCA) as the comparative context.

To remain within Zenodo file-count limits while preserving usability, the deposited materials are provided mainly as category-level ZIP archives rather than as a large number of separate files. The README file is provided as an uncompressed text document for immediate inspection. Each ZIP archive groups closely related files belonging to one analytical module, including multiomics, external validation, GEM robustness, LINCS, SLC16A1 docking/benchmark outputs, SLC25A1 exploratory docking outputs, scripts, logs, and environment snapshots.

The deposited materials include:(1) processed multi-omics tables for PRAD, BRCA, and merged analyses;(2) external validation outputs from BRCA_METABRIC and PRAD_SU2C;(3) GEM robustness summaries, reaction-proxy maps, and blocked-precursor diagnostics;(4) GSE92742-only LINCS perturbational-support outputs for SLC16A1;(5) SLC16A1 redocking, comparator, active–decoy benchmark, reranking, and consensus-scoring outputs;(6) SLC25A1 exploratory docking summaries and cross-box evaluation outputs;(7) Python, R, and shell scripts used for analysis;(8) terminal log files documenting major analytical steps; and(9) environment snapshots for the primary reproducible conda environments (uroc_v3 and uroc_gem) together with system-level R and software snapshots.

Raw public datasets were not re-deposited in this record and should be obtained from their original sources, including GDC/TCGA-PRAD, GDC/TCGA-BRCA, GTEx, PDC/CPTAC, Metabolomics Workbench, cBioPortal/METABRIC, SU2C PRAD, LINCS GSE92742, ChEMBL, Open Targets, and Human1/Human-GEM, as described in the manuscript and Supplementary Information.

This record is deposited as a restricted-access reviewer package. Access to the deposited files may be provided to journal editors and reviewers through a reviewer-specific access link during peer review.