Introduction to Motif Discovery and Transcription Factor Binding Site Analysis

Bioinformagician
Bioinformagician
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Published 2023-08-28
In this comprehensive video, I cover basics of motifs, transcription factors, regulatory regions (promoters, enhancers, silencers, insulators), how motifs are represented and questions that Transcription Factor Binding Site (TFBS) analysis can help to answer. Furthermore, I list down various available tools to perform motif discovery and motif databases followed by demonstrating how to find enriched de novo and canonical motifs in regions quantified by ChIP sequencing using #Homer. Additionally, I also demonstrate how to find instances of motifs of interest in the peaks.
This video is in collaboration with geneXplain GmbH (youtube.com/@geneXplain) which is one of the worldwide known providers of top bioinformatics, systems biology and cheminformatics databases, software and services.
I hope you find this video helpful! Leave your thoughts in the comment section below!

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▸ Types of high throughput data:
   • Types of High Throughput Data in Bioi...  

▸ ChIP-Seq file format:
   • Understanding File Formats in Bioinfo...  

▸ Homer Vignette:
homer.ucsd.edu/homer/ngs/peakMotifs.html

▸ Data used for demonstration:
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE1293…

▸ Link to Code:
github.com/kpatel427/YouTubeTutorials/blob/main/ru…

Chapters:
0:00 Intro
1:44 What are motifs?
4:37 What are Transcription Factors?
6:49 Structure of a gene and regulatory regions
9:37 Why is there a need for gene regulation?
12:35 Different ways to represent Motifs or Transcription Factor Binding Sites
16:37 When to perform a Transcription Factor Binding Site Analysis?
19:22 Tools available to perform motif analysis
20:52 Motif databases
21:14 Case study for demonstration using Homer
23:00 Fetch data from NCBI GEO
25:40 About Homer and notes on installation
30:06 Following Homer instructions to find motifs in genomic regions
31:12 Manipulate peak file to get it into the acceptable format
34:32 Run Homer script to find motifs
35:58 Looking at resulting files
38:10 Understanding Homer’s de novo motif finding results
41:08 Understanding Homer’s known motif (canonical) finding results
44:00 Find which peaks do a specific motif bind to?
45:14 Method 1 to find motif instances
47:50 Method 2 to find motif instances

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To get in touch:
Website: bioinformagician.org/
Github: github.com/kpatel427
Email: [email protected]

#bioinformagician #bioinformatics #homer #genexplain #genexplainplatform #transfac #motif #motifanalysis #tfbs #chipseq #epigenomics #epigenome #atacseq #singler #10x #alleles #bam #vcf #gvcf #gatk #haplotype #alleles #variantcalling #geneticvariants #mutations #gff3 #gff #gtf #sam #bam #phred #fasta #fastq #singlecell #10X #ensembl #biomart #annotationdbi #annotables #affymetrix #microarray #affy #ncbi #genomics #beginners #tutorial #howto #omics #research #biology #GEO #rnaseq #ngs
All Comments (10)
  • @adrielhernando2162
    Thanks for the very clear explanation! Especially the tutorial on how to use HOMER with a case study!!
  • @madhur1002
    Thank you. All your videos are amazing.Very well put with clear concepts and methodology.
  • @nk12987
    Hey! Thank you for this video..can you please upload a complete step wise video on ATAC seq analysis using command line and if possible a video on whole exome sequence analysis too😁 ... thank you.... you are a life saviour 😅
  • @keshavprasad6485
    Hi Thanks for the video. Do you think this analysis and set of tools could be carried out in single cell data as well? for Ex: scATACseq data?
  • @mikiallen7733
    thanks Mam for such interesting coverage , however, would one be able using the tools that you have explained above to do a complete analysis of a drug within the class of anti-psychotic/neuroleptics to understand more about the effects of such class of drugs on gene expression as well as short and long-term impacts(including longevity) of a regular usage of such drugs ? and what about the case for the first-line treatment options using anti-depressants ? your input is highly appreciated