From Toxicogenomics Data to Cumulative Assessment Groups: A Mechanistic Framework for Chemical Grouping

Supplementary Material

This dataset provides supplementary material for the manuscript "From Toxicogenomics Data to Cumulative Assessment Groups: A Mechanistic Framework for Chemical Grouping".

The paper is available at BioRxiv with the DOI:

Contents:

1. SQLite Database 

Filename: 2023_03_20_ctd_pubchem_sqlite.db

The SQLite database integrates manually curated and modified data from the Comparative Toxicogenomics Database (CTD, https://ctdbase.org/) (Davis et al. 2024; https://doi.org/10.1093/nar/gkae883) and PubChem (https://pubchem.ncbi.nlm.nih.gov/). This database serves as the foundation for constructing CGPD Tetramers and facilitates chemical grouping across diverse regulatory contexts.

The database was uploaded for reproducibility purposes to ensure the reproducibility of the analyses presented in the study.The Snapshot data of the datasets was March 20th, 2023.

Table summarizing the structure of the SQLite database. The data in the tables starting with ’CID’ was collected from PubChem and originated from different source files. Tables starting with ’CTD’ originated from CTD. The snapshot date of the data set is March 20th, 2023.

Table Name
# Columns
# Entries

CID_chemicalproperties
6
12041

CID_IDs
6
16332

CTD_anatomy
9
1844

CTD_chem_gene_ixns
12
2487743

CTD_chem_gene_ixn_types
4
53

CTD_chem_go_enriched
13
6237303

CTD_chemicals
8
175847

CTD_chemicals_diseases
10
8276711

CTD_chem_pathways_enriched
11
1483203

CTD_diseases
9
13270

CTD_diseases_pathways
5
609539

CTD_exposure_events
43
204735

CTD_exposure_studies
10
3304

CTD_genes
8
589897

CTD_genes_diseases
9
100715108

CTD_genes_pathways
4
135783

CTD_pathways
2
2567

CTD_pheno_term_ixns
13
340861

NCBI_GO
3
105515336

2. Supplementary Figures and Tables

Filename: Canzler_et_al_Grouping_Supplementary_Material.pdf

The PDF file contains detailed tables and graphical representations of the results and methods used in the study.

3.  Disease Tissue associations

Filename: Disease_Tissuegroups.tsv

The TSV file provides a mapping of disease terms to corresponding tissue groups where this disease is manifested.For example:

D011660    Pulmonary Heart Disease    Cardiovascular system

Diseases may be linked to one or multiple tissue groups; otherwise, they default to all tissue groups.