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Current and up-coming analysis tools for the NCI-60 in CellMiner: Resources for data integration and systems pharmacology

William C. Reinhold

The CellMiner web-application; a suite of tools that provides rapid access to multiple forms of molecular and pharmacological data available for the NCI-60. These tools also aid in the integration of this high-throughput data in a manner doable by the non-bioinformaticist. The integration tools are accessed in the “NCI-60 Analysis Tools” section. These include the “Cell line signature” tool, which provides i) transcript levels, ii) compound activities, and iii) microRNA levels for the NCI-60. Access to the exome sequencing data will be demonstrated, including use of the “Graphical output for DNA:Exome sequencing”. The individual forms of data may in turn be integrated using the “Cross-correlation” tool for up to 150 genes (transcript levels), microRNA levels and drug activities. The data may also be integrated using “Pattern comparison”, which allows the input of any pattern (for the NCI-60), and from that pattern correlates all gene transcript and microRNA levels, and compound activities. Several indevelopment tools are also demonstrated. The first of these are “aCGH copy number” for the determination of DNA copy number variations. Second is “Genetic variant summation”, which provides a summation of mutations in a pathway for up to 150 genes. Third is “Genetic variant versus drug visualization” which provides rapid visualization of gene variant versus drug relationships. Each of these tools permits the user to search for potential relationships in a manner specific to their area of expertise and interest. Expertise in computer science or bioinformatics is not required. The data is available at no cost to the scientific public.