A real-data-anchored axolotl–naked mole-rat biosignature for constrained regenerative-safety drug-repurposing benchmarks

This package contains the real-data-only LaTeX submission source, supplementary material, validation tables, downloaded public GEO matrices when available, and code references for the axolotl/naked mole-rat regenerative-safety biosignature manuscript. Synthetic candidate maps and synthetic benchmark metrics from earlier exploratory drafts are intentionally excluded from this deposit package. Candidate prioritization in the manuscript uses a real ChEMBL mechanism-derived target-modulation matrix. Main folders: - `academia_biology_latex_source_realdata/`: journal LaTeX source with `main.tex`, `references.bib`, figures and tables. - `academia_biology_supplement_realdata/`: supplementary LaTeX source. - `data_real_geo/`: downloaded public GEO supplementary/RAW matrices used for direct reanalysis, when present locally. - `data_orthology/`: downloaded NCBI RefSeq proteomes, curated DIAMOND reciprocal-hit inputs and curated OrthoFinder outputs. - `scripts/create_realdata_latex_submission_package.py`: reproducible script used to regenerate the real-data-only LaTeX package and figures. - `scripts/run_real_geo_chembl_reanalysis.py`: direct GSE92429/GSE132642 and ChEMBL mechanism-matrix reanalysis script. - `scripts/run_reciprocal_diamond_orthology.py`: targeted DIAMOND reciprocal protein validation for curated biosignature anchors. - `scripts/fastq_reprocessing_hpc_workflow.sh`: HPC/WSL workflow for complete FASTQ reprocessing from SRA when sufficient storage and references are available. Reproducibility status: - GEO matrix/RAW-CSV reanalysis: included and used for the submitted figures/tables. - ChEMBL target-modulation matrix: real mechanism records only; no synthetic pharmacological labels are included. - Targeted orthology validation: included for selected feature anchors using DIAMOND and a curated OrthoFinder run; this is not a full all-Trinity transcript orthology map. - FASTQ-level reprocessing: SRA RunInfo preflight tables and a complete executable workflow are included. The full end-to-end FASTQ run is not claimed as locally completed because SRP065567 and SRP201320 require approximately 743 GB of compressed SRA input before FASTQ expansion and reference indexing. Recommended rebuild order: 1. Run `python scripts/run_real_geo_chembl_reanalysis.py`. 2. Run `python scripts/run_reciprocal_diamond_orthology.py`. 3. Run `python scripts/create_realdata_latex_submission_package.py`. 4. Compile `main.tex` and `supplementary_material.tex` with `pdflatex`, `bibtex`, `pdflatex`, `pdflatex`.