Two major advances have recently taken place in biological research that underscore the need for a Bioinformatics Facility Core (BFC) in the Southwest Environmental Health Sciences Center (SWEHSC). One is the availability of very large amounts of sequence data from various genome projects. The second is the collection of very large biological data sets such as (i) gene and tissue microarray data for testing gene and protein expression profiles, (ii) sequence, structural and molecular interaction data from the analysis of proteins and protein complexes, and (iii) the acquisition of data on sequence polymorphisms (SNPs) that influence disease, drug sensitivities and other biological properties of cells and tissues. To use these data effectively, investigators need to store, share and interpret these data sets, and assistance with (a) the development of local computer tools for data storage and analysis, (b) accessing remote databases and information on the human and mouse genomes and proteins, (c) data analysis and modeling and (d) suitable experimental designs for large data sets e.g. cDNA spotted microarrays for gene expression measurements. The overall objectives of the BFC are to meet the collective needs of SWEHSC researchers, students, and laboratory staff with computational support for management, analysis, display and integration of these genomic and proteomics data. These objectives will be achieved through the following Specific Aims: 1. Design or use existing data models for informatics support of proteomics and genomics data;use these models to develop relational databases and XML formats for storing and the sharing all of the mass spectrometry data generated by the Proteomics Facility Core (PFC) and genomics data generated by the Genomics Facility Core (GFC);integrate the proteomics and genomics data, and provide straightforward web access to these data and data analysis tools to SWEHSC investigators. 2. Advance the analysis of SEQUEST searches and results of cDNA microarray experiments by providing more detailed and specific information about the peptides and genes under investigation, and the affected metabolic pathways and regulatory systems. 3. Provide tools for dynamic queries/data mining to discover data relationships and patterns hi the Proteomics and Genomics data sets. These search tools will provide (i) new molecular markers for detection of disease and of environmental responses, (ii) a basis for developing new hypotheses, and (iii) ways to advance the research goals of SWEHSC researchers.
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