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Supplemental Information

Density plot of lactate dehydrogenase (LDH) activity (%) across human and rat in vitrohepatic experiments from the OPEN TG-GATEs Project

About 86% of experiments were indicated normal in the range of 95%-105% and the remaining 14% were cytotoxic cases. 95% and 105% are cut-offs that appear at 5% of left and right tails, respectively.

DOI: 10.7287/peerj.preprints.27839v1/supp-1

Ratios plot of BMDt/BMDa for each NTP experimental group determined with T384 gene set

DOI: 10.7287/peerj.preprints.27839v1/supp-2

Ratios plot of BMDt/BMDa for each NTP experimental group determined with T1500 gene set

DOI: 10.7287/peerj.preprints.27839v1/supp-3

PCA plots for 158 chemicals of the Human in vitrodataset of Open TG-GATEs showing similarity of patterns when all genes are used and when only T1000 genes are considered

DOI: 10.7287/peerj.preprints.27839v1/supp-4

Explanation of the different iterations for computing prior scores

DOI: 10.7287/peerj.preprints.27839v1/supp-5

Discussion of LDH% vs. dose distribution for selection of binarization thresholds needed for the binary classification models

DOI: 10.7287/peerj.preprints.27839v1/supp-6

List of the 258 clusters produced in the study and the set of grouped genes in each cluster. Each line represents a different cluster of genes

DOI: 10.7287/peerj.preprints.27839v1/supp-7

The list of T1500 genes which includes T1000 as the top-ranked 1000 genes

DOI: 10.7287/peerj.preprints.27839v1/supp-8

Detailed quantitative comparison of gene expression space coverage

DOI: 10.7287/peerj.preprints.27839v1/supp-9

Ranked list of T1000 genes with annotations drawn from the Protein Atlas

DOI: 10.7287/peerj.preprints.27839v1/supp-10

Detailed performance evaluation scores of each of the gene sets when applied to the external kidney dataset from Open TG-GATEs

DOI: 10.7287/peerj.preprints.27839v1/supp-11

Additional Information

Competing Interests

Jianguo Xia is an Academic Editor for PeerJ.

Author Contributions

Othman Soufan conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Jessica Ewald conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Charles Viau contributed reagents/materials/analysis tools, approved the final draft, manuscript review.

Doug Crump contributed reagents/materials/analysis tools, approved the final draft, manuscript review.

Markus Hecker contributed reagents/materials/analysis tools, approved the final draft, manuscript review.

Niladri Basu conceived and designed the experiments, contributed reagents/materials/analysis tools, approved the final draft.

Jianguo Xia conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

Data is available at Open TG-GATEs and GEO, accession No. GSE45892.

Funding

This study was funded by Genome Canada, Génome Québec, Genome Prairie, the Government of Canada, Environment and Climate Change Canada, Ministère de l'Économie, de la Science et de  l'Innovation du Québec, the University of Saskatchewan, and McGill University. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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