How to extract epigenetic features from ENCODE

Question

[Ina]

I am trying to use ENCODE to get epigenetic features like H3K4me3 position information and CTCF binding information from ChIP-Seq assay for a particular chromosome coordinate. I used the "search by region" option under "Data" in ENCODE to provide the coordinates like, for example for K562 cell type :

chr3:46399154-46399176

I do not know how to interpret the results I get for this coordinate. Like should I confirm that this sequence has CTCF binding feature if CTCF appears in the result? Kindly help as I am totally new to this area.

[jared.andrews07]

You can just look at the signal for the mark/TF of interest in a genome browser if you just want to check that it's believable.

[Ina]

Thank you @jared.andrews07 Do you mean the signal p-value? There are quite a few like "ENCFF145REP signal p-value rep 1" and "ENCFF118JQZ signal p-value rep 1,2" Which one should I look for?

[Ina]

Is it possible for you to add a sample if it's not a trouble for you please.

[jared.andrews07]

Go to the UCSC genome browser and select hg19. Much of the ENCODE data is from hg19, so that's what I'm using for this example. Use the track search. Following your example, search for "K562 CTCF". Choose as many of the tracks as you want. View them on the browser for your region of interest, in this case "chr3:46399154-46399176". This region doesn't appear to have much CTCF binding in K562 cells on hg19.

You can add whatever tracks you want and save it as a session to come back to it again and again. Spot check your regions of interest as needed. If you have many of them, you could either use a program to snapshot each region and quickly peruse the images or take a more involved, programmatic approach.

[Ina]

Thanks a lot jared.andrews07

Answer 1

[ATpoint]

Alternatively, given you work in human, you can also visit ReMap ( http://tagc.univ-mrs.fr/remap/index.php?page=browse ) which is a database collecting published ChIP-seq data, offering browser tracks and peak lists and a webtool to intersect your coordinates with the database. This is probably way more convenient than these (sometimes cryptic) ENCODE files.

[Ina]

Thanks for your inputs ATpoint