Question: Comparing Protein-DNA binding species at specific time points
0
gravatar for Hushus
23 months ago by
Hushus 20
Hushus 20 wrote:

Hello world,

I have the following [from different published sources]:

1) [Protein of Interest] TF binding data at different time points in development (ChIP)

2) Histone modifications at different time points in development (ChIP)

3) Other proteins binding data that are enriched from MEME with (1) (ChIP)

I would like to see if the bound sites of (1) relate to (2) and (3).

Question A) Is there a simple designed pipeline for this?

Question B) How would you find % enrichment at (1) sites. As in H3K4me is enriched at 60% of (1) sites. Would you do a BED vs. BED of the binding peaks and see how many of them relate to each other or is there another better tool?

chip-seq chip • 512 views
ADD COMMENTlink modified 23 months ago by Hussain Ather940 • written 23 months ago by Hushus 20
1
gravatar for Hussain Ather
23 months ago by
Hussain Ather940
National Institutes of Health, Bethesda, MD
Hussain Ather940 wrote:

You could try finding the colocalization between (1) and (2) or (3). A few tools I can think of are gat and intervalstats.

ADD COMMENTlink written 23 months ago by Hussain Ather940
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