Abstract 5327: Using CellMiner for gene expression, DNA copy number, microRNA transcript levels, variant status, drug activity, and their integration for systems pharmacology for the NCI-60

Abstract

Abstract Molecular biology and pharmacology are being transformed by high-throughput data. Access, and integration of this data, however, remains difficult. The NCI-60 cancerous cell lines are arguably the premier model for data integration and systems pharmacology. To make this data accessible for both bioinformaticists and non-bioinformaticists, we have developed the CellMiner set of web-based tools (http://discover.nci.nih.gov/cellminer). These tools currently or in the near future will provide “Cell line signatures” for gene and microRNA transcript expression, DNA copy number variation, genetic variation, and drug or compound activity. This data includes relative levels of transcript expression for 26,065 genes, 360 microRNAs, activities of 19,940 compounds including 110 Food and Drug Administration (FDA)-approved and 53 in clinical trial drugs, and percent conversions of 16,381 genetic variants (both germline and somatic). Current or upcoming tools facilitating the combination of this data include i) “Pattern comparison”, which provides correlations to a users input pattern to transcript and microRNA expression and compound/drug activity, ii) “Cross correlation”, which provides all correlations between up to 150 input genes, microRNAs, and compounds or drugs, iii) “Genetic variation versus drug visualization”, which provides a rapid visualization of potential drug: gene DNA variant relationships, and iv) “Genetic variant summation”, which provides a synopsis of mutational burden on any pathway of interest for up to 150 genes. These tools allow the user to flexibly query the data for potential relationships between molecular and pharmacological parameters, in a manner specific to that users area of expertise and interest. Citation Format: William C. Reinhold, Margot Sunshine, Sudir Varma, Joel Morris, Kurt Kohn, James Doroshow, Yves Pommier. Using CellMiner for gene expression, DNA copy number, microRNA transcript levels, variant status, drug activity, and their integration for systems pharmacology for the NCI-60. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5327. doi:10.1158/1538-7445.AM2014-5327