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