Novel Tools for the Vertical Analysis of Genomic Data

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Due to the scarcity of good bioinformatics professionals, many expensivegenomics experiments remain under-analyzed. The goal of this proposal is to provide a suite of turnkey bioinformatics tools that: i) can process extremely large amounts of data as those coming from current high-throughput technologies such as microarrays, and ii) allow vertical inferences assembling system level information from component level data. The work proposed here will provide a novel database and associated data mining tools allowing: (1)Translation of gene expression profiles into functional profiles showing how various cellular functions are changed in the given condition and assessing their statistical significance, (2) Discovering those biological processes whose interaction in a given condition is significantly different their normal interaction. (3)Identifying those pathways that are most likely to be biologically relevant in agiven experiment and quantitatively assessing their impact. (4)Validating high-throughput experiments, such as microarrays, by checking the consistency of their results against existing biological knowledge (5) In-silico whole-body data mining techniques able to provide in a short time an expression profile of any given gene across all tissues of interest.The broader impact aspects of this proposal include the following:1. Enhance the research infrastructure by constructing and maintaining a public database with advanced data mining capabilities. 2. Cross-train researchers in computer science and biology.3. Broaden the participation of under-represented groups by: i) recruiting Ph.D. students ii) undertaking two annual recruitment visits to specific minority-serving institutions; iii) organizing an open house for disadvantaged K-12 students; and iv) targeted advertising of the positions funded through this project. 4. Broadly disseminating scientific knowledge by: i) providing a web interface to the tools developed during this project allowing the scientific community to access them easily ; and ii)organizing an annual multidisciplinary conference bringing together computer scientists and biologists.