CellMinerCDB for Integrative Cross-Database Genomics and Pharmacogenomics Analyses of Cancer Cell Lines

• Published in: iScience Vol. 10; pp. 247 - 264
• Main Authors: Rajapakse, Vinodh N., Luna, Augustin, Yamade, Mihoko, Loman, Lisa, Varma, Sudhir, Sunshine, Margot, Iorio, Francesco, Sousa, Fabricio G., Elloumi, Fathi, Aladjem, Mirit I., Thomas, Anish, Sander, Chris, Kohn, Kurt W., Benes, Cyril H., Garnett, Mathew, Reinhold, William C., Pommier, Yves
• Format: Journal Article
• Language: English
• Published: United States Elsevier 21.12.2018
• Subjects: Biological Database; Bioinformatics; Genomics; Cancer Systems Biology
• ISSN: 2589-0042; 2589-0042
• DOI: 10.1016/j.isci.2018.11.029

CellMinerCDB provides a web-based resource (https://discover.nci.nih.gov/cellminercdb/) for integrating multiple forms of pharmacological and genomic analyses, and unifying the richest cancer cell line datasets (the NCI-60, NCI-SCLC, Sanger/MGH GDSC, and Broad CCLE/CTRP). CellMinerCDB enables data queries for genomics and gene regulatory network analyses, and exploration of pharmacogenomic determinants and drug signatures. It leverages overlaps of cell lines and drugs across databases to examine reproducibility and expand pathway analyses. We illustrate the value of CellMinerCDB for elucidating gene expression determinants, such as DNA methylation and copy number variations, and highlight complexities in assessing mutational burden. We demonstrate the value of CellMinerCDB in selecting drugs with reproducible activity, expand on the dominant role of SLFN11 for drug response, and present novel response determinants and genomic signatures for topoisomerase inhibitors and schweinfurthins. We also introduce LIX1L as a gene associated with mesenchymal signature and regulation of cellular migration and invasiveness.