Motif discovery and enrichment in genomic regions (ChIP-Seq) using TRANSFAC
In this comprehensive video, we perform motif discovery and find enriched transcription factor binding sites (TFBS) using TRANSFAC in genomic regions of interest i.e ChIP-Seq peaks. geneXplain's point and click interface requires no programming to run the workflows and generate meaningful insights from high throughput data. In this demonstration, we run the workflows using geneXplain's platform and generated detailed insights on the TFBS of interest.
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.
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▸ Part 1 of this video:
• Introduction to Motif Discovery and T...
▸ What are Position Weight Matrices (PWMs)?:
• Introduction to Motif Discovery and T...
▸ Data used for demonstration:
https://www.ncbi.nlm.nih.gov/geo/quer...
▸ Contact geneXplain:
https://genexplain.com/contact/
Chapters:
0:00 Intro
0:47 Case Study
1:36 About geneXplain
2:16 Searching for enriched TFBS using TRANSFAC
3:03 Exploring geneXplain’s platform
5:13 Uploading the data onto the platform
6:53 Subsetting data using filters
8:18 Converting peaks in tabular format to track format
10:23 Running the workflow to find enriched TFBS using TRANSFAC
11:58 Exploring the Sites Search Summary results
14:06 Exploring the resulting transcription factors
15:36 Exploring instances of PWMs of interest in more detail
18:32 Visualizing TFBS in a genome browser
20:14 Mapping peaks to genes
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To get in touch:
Website: https://bioinformagician.org/
Github: https://github.com/kpatel427
Email: [email protected]
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