Gene Regulation

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Workshop Objective:

This 4-hour workshop provides an overview of resources and search strategies on transcriptional regulation. Emphasis will be given to HSLS-licensed TRANSFAC/Match and Correlation Engine software, as well as open-access tools such as the UCSC genome browser and Cistrome data browser

Participants will learn to

  • retrieve information linked with a transcription factor
  • retrieve the promoter sequence for a gene of interest
  • extract transcription regulatory elements--promoters, enhancers, and silencers associated with a gene of interest
  • identify the transcription factor binding site(s) present in a DNA sequence
  • identify transcription factor binding sites present in a ChIP-Seq dataset (motif discovery)
  • identify upstream regulatory transcription factors for a differentially expressed gene data set
  • start with a gene expression data set and find correlated studies with gene perturbation experiments (knock-out, knock-down, etc.) available in the GEO database
  • start with a ChIP-Seq data set and find factors that have a significant binding overlap with the ChIP-Seq peak set

Target Audience:

Experimental biologists studying epigenetic regulation on gene expression and interested in analyzing promoter and enhancer sequences. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with command line interface is required.

Workshop Requirements:

Workshop Guide:

Attribution:

Please include the following statement in the acknowledgments section for all publications, posters, and presentations: Data analysis was performed using {name of software} software licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh.

Class Type