About this Class

Understanding the biology in transcription factor binding site data requires a comprehensive and integrated approach and must be supplemented with highly-curated data content from multiple sources. Genomatix is a computational biology company with a 22-year history of developing tools and data content for understanding the molecular mechanisms of eukaryotic gene expression. This two-day class will provide an easy-to-use bioinformatics software platform for the detailed analysis of promoters and transcription factor binding sites. This two-day lecture and training workshop will introduce students to the rich applications for transcription factor binding site (TFBS) analysis using the Genomatix platform. This course is broken down into a morning and an afternoon session. NOTE: Registration and attendance for the day one session is required to attend the day two session. The day one session will focus on promoter annotation, basic transcription factor binding site analysis, and comparative genomics. Covered topics: promoter annotation and alternative promoters; using tissue activity data to select promoters (programs: ElDorado, Gene2Promoter); TFBS analysis with additional lines of evidence (MatInspector, MatBase); promoter orthologs and analysis of conserved TFBSs (Common TFs, DiAlignTF). The day two session will focus on regulatory cassettes and genome-wide analysis of ChIP-Seq data. Covered topics: analysis of conserved gene regulatory cassettes (FrameWorker, ModelInspector); TFBS and TFBS pattern overrepresentation in ChIP-Seq peaks (Overrepresented TFs); gene neighbor and promoter overlap annotation of ChIP-Seq peaks (Annotation & Statistics). Register