This workshop provides an overview of resources and search strategies for transcriptional regulation. Emphasis will be placed on HSLS-licensed TRANSFAC/Match and Correlation Engine software, as well as open-access tools like the UCSC Genome Browser and the Cistrome Data Browser.
Target Audience:
Experimental biologists interested in analyzing bulk RNA-Seq and/or ChIP-Seq data, whether generated through their own experiments or retrieved from repositories such as GEO, will find this workshop particularly useful. The software covered in the workshop features a user-friendly, point-and-click graphical user interface, eliminating the need for programming experience or familiarity with the command-line interface.
Upon completing this class, you should be able 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
Recording status
This class will be recorded and shared with attendees.
Class Materials
Class materials will be shared with attendees.