Introduction to Motif Discovery and Transcription Factor Binding Site Analysis

Explore the fundamentals of motif discovery and transcription factor binding site analysis in this comprehensive 52-minute video tutorial. Delve into the basics of motifs, transcription factors, and regulatory regions, including promoters, enhancers, silencers, and insulators. Learn how motifs are represented and discover the questions that Transcription Factor Binding Site (TFBS) analysis can answer. Gain insights into various tools for motif discovery and explore motif databases. Follow along with a practical demonstration using Homer to find enriched de novo and canonical motifs in regions quantified by ChIP sequencing. Discover methods for identifying instances of motifs of interest in peaks. Enhance your understanding of gene regulation and epigenomics through this collaborative presentation with geneXplain GmbH, a renowned provider of bioinformatics, systems biology, and cheminformatics resources.

Intro
What are motifs?
What are Transcription Factors?
Structure of a gene and regulatory regions
Why is there a need for gene regulation?
Different ways to represent Motifs or Transcription Factor Binding Sites
When to perform a Transcription Factor Binding Site Analysis?
Tools available to perform motif analysis
Motif databases
Case study for demonstration using Homer
Fetch data from NCBI GEO
About Homer and notes on installation
Following Homer instructions to find motifs in genomic regions
Manipulate peak file to get it into the acceptable format
Run Homer script to find motifs
Looking at resulting files
Understanding Homer’s de novo motif finding results
Understanding Homer’s known motif canonical finding results
Find which peaks do a specific motif bind to?
Method 1 to find motif instances
Method 2 to find motif instances