A major goal in efforts to understand the mechanisms by which signal transduction pathways regulateprograms of gene expression is to identify their direct target genes and to determine the specific componentsof the transcriptional machinery that are recruited to these genes in response to regulatory signals. Tosupport these goals, the Transcriptional Genomics Core will provide three complementary services to PPGinvestigators; conventional gene expression (Chip) microarray analysis, recently developed genomic (ChlPChip)microarray analysis, and associated Bioinformatics support for experimental design oversight and dataanalysis. 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 tospecific promoter sequences in living cells. The PPG Transcriptional Genomics Core will fabricate murineintergenic/promoter microarrays to allow genome-wide location analysis of PPARs, NCoR, SMRT, and othertranscription factors of relevance to this application. Effective utilization of genome-wide approachesrequires an understanding of the strengths and limitations of these technologies, particularly with respect tosources of error and the number of experimental replicates that are required to develop gene lists at definedand acceptable false positive and false negative rates. Personnel within the PPG Transcriptional GenomicsCore will interact with scientists within each of the Projects to provide experimental design oversight focusedon these issues. Once microarray experiments are performed and raw data is collected, the TranscriptionalGenomics Core will utilize standard tools to develop gene lists at specified levels of confidence and performsecondary analysis (e.g., Gene Ontology analysis, mapping to KEGG pathways, etc.). The TranscriptionalGenomics Core will provide a database infrastructure for data storage and retrieval to allow integration ofdata collected across the PPG and the application of more sophisticated bioinformatics approaches outlinedin each of the Projects.
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| Hartmann, Phillipp; Hochrath, Katrin; Horvath, Angela et al. (2018) Modulation of the intestinal bile acid/farnesoid X receptor/fibroblast growth factor 15 axis improves alcoholic liver disease in mice. Hepatology 67:2150-2166 |
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