Abstract 3749: Uses and update for CellMiner, a tool for access to and comparison of molecular data and pharmacological response for the NCI-60

Abstract

Abstract Integration and understanding of genomic and proteomic data and their relationships with and influences on pharmacology have become key components of cancer research and its translation to therapeutics. Nonetheless, multiple significant obstacles need to be overcome for both their integration and understanding. The NCI-60 cancerous cell lines provide a premier opportunity in this area due to the scope and quality of the available data. CellMiner (http://discover.nci.nih.gov/cellminer) is a web-application that allows the user to rapidly access data for relative levels of transcript expression for 25,772 genes, genetic variants for 16,568 genes, transcript expression for 360 microRNAs, protein levels for 94 genes, and DNA copy number (from aCGH) for 23,413 genes. In addition, it provides concentration-response activities for 20,002 compounds including 114 Food and Drug Administration (FDA)-approved, 55 clinical trial, and 349 known mechanism-of-action drugs. Here we present our latest CellMiner update along with examples of data integration that provide enhanced understanding in the systems biological sense. Included in the tool updates are i) the upcoming “Protein mean value” cell line signature tool, ii) the recently introduced “Gene DNA copy number” tool, iii) introduction of the “Cross-correlations of transcripts, microRNAs, and drugs” tool, iv) the provision of additional forms of data in the standard output for the “Pattern comparisons” tool, and v) upgrades of the “Genetic variant versus drug visualization” tool allowing the user to query for all drugs significantly correlated to genomic variants for the whole human genome (or visa versa). Examples of data integration will include SLFN11 expression versus the activities of DNA-damaging drugs, RAS activation considering three forms of molecular data, and PTEN knockdown and pharmacological connection (also using three forms of molecular data). The data and tools are or shortly will be publicly available at CellMiner. Citation Format: William C. Reinhold, Margot Sunshine, Sudir Varma, Vinodh Rajapakse, James Doroshow, Joel Morris, Yves Pmmier. Uses and update for CellMiner, a tool for access to and comparison of molecular data and pharmacological response for the NCI-60. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3749. doi:10.1158/1538-7445.AM2015-3749