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.
I hope you find this video helpful! Leave your thoughts in the comment section below!

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▸ Part 1 of this video:

▸ What are Position Weight Matrices (PWMs)?:

▸ Data used for demonstration:

▸ Contact geneXplain:

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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[ManasviniSubramanian]

very informative video, thanks ma'am. kind request to post a video on how to perform differential binding analysis on ATAC seq and ChIP seq, and any correlational analysis of chip seq and atac seq, if possible. Please!!!

[anaidmontesinos]

I created my count but we have to pay. I to use it. Do you have your license of this software?

[ShwetaPandey-by]

Hey! you make nice videos, just a request, would you please make on enrichment analysis and why background genes are needed as a baseline? Please share some relevant resources to understand it better from the basics.

[DataDude-oisi]

Mam I'm currently studying BSc Bioinformatics and I'm confused about which college should I apply for can you make. Video on MSc For Bioinformatics colleges in India and you have done your MSc from Khalasa college can you plz provide some information about it and also how to apply and which University to apply for outside India

[tolga]

Cell-Cell-Communication Tutorial please