Introduction to Motif Discovery and Transcription Factor Binding Site Analysis
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- čas přidán 29. 06. 2024
- 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 ( / @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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The content presented on this CZcams video channel is designed exclusively for educational purposes. It should be noted that the creator of the channel makes every possible effort to ensure the accuracy and credibility of the information shared. However, due to the ever-evolving nature of knowledge and certain subjects, occasional inaccuracies or outdated information might occur. Therefore, viewers are strongly advised to complement the provided content with their personal research and seek guidance from qualified professionals or experts before making any decisions or inferences based on the information presented in the videos. Moreover, the perspectives and opinions expressed in the videos are those of the creator alone. They do not necessarily reflect the viewpoints of any affiliated organization, institution, or entity associated with the creator.
▸ Types of high throughput data:
• Types of High Throughp...
▸ ChIP-Seq file format:
• Understanding File For...
▸ Homer Vignette:
homer.ucsd.edu/homer/ngs/peakM...
▸ Data used for demonstration:
www.ncbi.nlm.nih.gov/geo/quer...
▸ Link to Code:
github.com/kpatel427/CZcamsT...
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
Like the videos I create? Show your support and encouragement by buying me a coffee:
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To get in touch:
Website: bioinformagician.org/
Github: github.com/kpatel427
Email: khushbu_p@hotmail.com
#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
Thanks for the very clear explanation! Especially the tutorial on how to use HOMER with a case study!!
Thank you. All your videos are amazing.Very well put with clear concepts and methodology.
Thank you
excellent video ! very informative
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 😅
Let's start a series on ATAC-SEQ data analysis
Hi it a mailing presentation. Thanks
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
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?
For scATAC-seq, use 'signac' r package
Have you use Fantom5 or enhancer atlas to predict for regulatory regions?
and do you know enhancer atlas? what are the differences between TRNANSFAC or JASPAR? thank you very much
Can you please tell how to convert the peak txt file to bed file?? please help??
TFIID, I guess (TBP is a part of TFIID)
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