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DrugMatrix and TG-Gates In vivo Data Integration

Jeremy Erickson, Frank Chao, Daniel Svoboda, Scott Auerbach

DOI: https://doi.org/10.22427/DATA-500-110-004-000-1

Related Publications

Auerbach, Scott S., Guojing Cong et. al, Completion of the DrugMatrix Toxicogenomics Database using ToxCompl, https://doi.org/10.22427/NTP-DATA-500-010-001-000-7

ToxCompl+, https://doi.org/10.22427/NTP-DATA-500-110-002-000-9

Publication

Abstract Background

This CEBS dataset release integrates treatment-level toxicogenomics and apical toxicology data from DrugMatrix and Open TG-GATEs into a common analysis resource for computational toxicology, toxicogenomics, machine learning, and data integration. It includes DrugMatrix gene-expression responses from Codelink RU1, Affymetrix RG230 2.0, and BioSpyder Whole Transcriptome/S1500+ TempO-Seq data extrapolated with Sciome GeniE, together with rat in vivo liver and kidney Affymetrix data from TG-GATEs. DrugMatrix coverage includes multiple tissues, while the TG-GATEs component is limited to rat in vivo liver and kidney studies. Gene-expression effects, clinical chemistry, and hematology endpoints are represented as log10 treated/control ratios, while histopathology findings are treatment-group average severity scores. Clinical-pathology and histopathology terminology are harmonized across sources, and relative-dose categories support cross-source modeling while preserving the underlying dose and duration information. Accessory files provide DTXSID-centered chemical identifiers and structures, molecular fingerprints, structural alerts, QSAR and other model predictions, and Generalized Read-Across results. Data are distributed as a gzip-compressed wide matrix with a feature dictionary, source-oriented tab-delimited files and ZIP archives, cross-dataset mapping files, and a queryable SQLite database containing a long-form integrated matrix and companion annotations. These formats support complete-matrix download, source-oriented use, targeted database queries, and construction of smaller analysis sets.

Data

Database

https://cebs-ext.niehs.nih.gov/cahs/file/download/paper/16422/drmat_tggat_matrix.db (54 GB)

Integrated Data Matrix

https://cebs-ext.niehs.nih.gov/cahs/file/download/paper/16422/2026_dmtg_matrix_data_rounded.txt.gz (583 MB)

Chemical Annotations

Supplemental Materials

Term Mapping

Annotations