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This file contains Supplementary Figure S1 (Correlation between downregulation of EGFR transcriptional target genes, and sensitivity to erlotinib at the high concentration after 6 hours); Supplementary Figure S2 (EGFR inhibitor and DNA damaging agents induce directionally opposing changes in EGR1 expression that are differentially associated with drug sensitivity); Supplementary Figure S3 (Representative 3D response surface plots for the gemcitabine-erlotinib combination in the indicated cell lines); Supplementary Figure S4 (Representative 3D response surface plots for the vorinostat-talazoparib combination in the indicated cell lines); Supplementary Table S1 (Validation of array-based measurements by qRT-PCR); Supplementary Table S2 (Genes with concerted changes in the same direction [upregulation or downregulation] 24 hours after treatment with each of the 15 drugs); and Supplementary Table S4 (Selected genes potentially mediating drug insensitivity to agents in the NCI TPW dataset).

The intracellular effects and overall efficacies of anticancer therapies can vary significantly by tumor type. To identify patterns of drug-induced gene modulation that occur in different cancer cell types, we measured gene-expression changes across the NCI-60 cell line panel after exposure to 15 anticancer agents. The results were integrated into a combined database and set of interactive analysis tools, designated the NCI Transcriptional Pharmacodynamics Workbench (NCI TPW), that allows exploration of gene-expression modulation by molecular pathway, drug target, and association with drug sensitivity. We identified common transcriptional responses across agents and cell types and uncovered gene-expression changes associated with drug sensitivity. We also demonstrated the value of this tool for investigating clinically relevant molecular hypotheses and identifying candidate biomarkers of drug activity. The NCI TPW, publicly available at https://tpwb.nci.nih.gov, provides a comprehensive resource to facilitate understanding of tumor cell characteristics that define sensitivity to commonly used anticancer drugs.Significance:The NCI Transcriptional Pharmacodynamics Workbench represents the most extensive compilation to date of directly measured longitudinal transcriptional responses to anticancer agents across a thoroughly characterized ensemble of cancer cell lines.