ajaygeetakumar/dili-toxicogenomics-expression

DILI Toxicogenomics Expression Data

Processed gene-expression matrices for drug-induced liver injury (DILI) research, mirrored here for programmatic loading. The authoritative, citable releases live on Zenodo (DOIs below); this Hugging Face copy is a convenience mirror.

The repository bundles two distinct processed datasets, each in its own subfolder.

unified-446-rat-liver/

Unified rat-liver microarray expression matrix for 446 DILI-relevant drugs, harmonized across four toxicogenomic sources (Open TG-GATEs, DrugMatrix-Affymetrix GSE57815, DrugMatrix-CodeLink GSE59923, Iconix CodeLink GSE8858).

• 5,859 unique (drug × dose × time) condition rows
• 24,531 Entrez gene IDs
• 446 / 446 drugs covered (100%)
• Affymetrix: RMA + BrainArray ENTREZG v22 (rat2302rnentrezgcdf_22.0.0)

File	Description
expression_446_per_condition.tsv	Main artifact — 5,859 conditions × (9 metadata + 24,531 genes)
expression_446_metadata.tsv	Metadata block only (no gene columns)
expression_446_genes.txt	Gene ID list
affy_tggates_single.tsv	TG-GATEs single-dose Affymetrix RMA matrix
affy_tggates_repeat.tsv	TG-GATEs repeat-dose Affymetrix RMA matrix
affy_dm_affy.tsv	DrugMatrix-Affymetrix (GSE57815) RMA matrix
microarray_drug_labels.csv	Per-drug DILI labels
tggates_rat_liver_invivo_compounds.txt	TG-GATEs rat-liver in-vivo compound list

Citable source: 10.5281/zenodo.20437046

eastman-pande-2019-crossspecies/

Processed RMA data for the faithful reproduction of Eastman & Pande 2019 (arXiv:1907.03041) — rat → human gene-expression prediction on Open TG-GATEs.

File	Description
rma_human.tsv	Human in-vitro liver RMA matrix
rma_rat.tsv	Rat in-vivo liver RMA matrix
pairs_human_Y.tsv	Paired human targets (Y)
pairs_rat_X.tsv	Paired rat features (X)
pairs_metadata.tsv	Pair metadata
pairs_splits.tsv	Train/val/test split assignments

Citable source: 10.5281/zenodo.20204514 (BrainArray Rat2302 ENTREZG v22 normalization).

Citation

If you use these data, please cite the corresponding Zenodo deposit(s) above.