A major goal in efforts to understand the mechanisms by which signal transduction pathways regulate programs of gene expression is to identify their direct target genes and to determine the specific components of the transcriptional machinery that are recruited to these genes in response to regulatory signals. To support these goals, the Transcriptional Genomics Core will provide three complementary services to PPG investigators;conventional gene expression (Chip) microarray analysis, recently developed genomic (ChlPChip) microarray analysis, and associated Bioinformatics support for experimental design oversight and data analysis. Conventional expression analysis will utilize commercially available microarrays (e.g., Affymetrix, Agilent and Illumina microarrays). Recent progress in combining the use of chromatin immunoprecipitation (ChIP) assays with DMA microarrays has allowed genome-wide analysis of transcription factor localization to specific promoter sequences in living cells. The PPG Transcriptional Genomics Core will fabricate murine intergenic/promoter microarrays to allow genome-wide location analysis of PPARs, NCoR, SMRT, and other transcription factors of relevance to this application. Effective utilization of genome-wide approaches requires an understanding of the strengths and limitations of these technologies, particularly with respect to sources of error and the number of experimental replicates that are required to develop gene lists at defined and acceptable false positive and false negative rates. Personnel within the PPG Transcriptional Genomics Core will interact with scientists within each of the Projects to provide experimental design oversight focused on these issues. Once microarray experiments are performed and raw data is collected, the Transcriptional Genomics Core will utilize standard tools to develop gene lists at specified levels of confidence and perform secondary analysis (e.g., Gene Ontology analysis, mapping to KEGG pathways, etc.). The Transcriptional Genomics Core will provide a database infrastructure for data storage and retrieval to allow integration of data collected across the PPG and the application of more sophisticated bioinformatics approaches outlined in each of the Projects.
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