Questions About Snps Enrichment On Important Regulators In Ucsc

Question

[J.F.Jiang]

Hello, everyone:

I want to get some annotations on some snps, using ucsc as primary annotation source.

As i know, UCSC defined some important regulators, such as Yale TFBS, and regulatory elements.

In some paper, i found that the author tended to consider some trascription factors as most important, such as c-Myc sirt6 c-Fox MAX...

it is true that TFBS of these transcription factors are very important, but how can we just consider these facotrs while neglecting the others? is there any evidence or reference could tell me the criteria of this classification?

and for regulatory elements such as cpgislandext...?

ps:i have used ANNOVAR doing the annotation of these snps, but i seemed that it was not clear enough to explain the exact reason linking to my investigated cancer target.

Thanks for sparing your time!

[Chris Penkett]

Are you looking for SNPs in regulatory regions? The Encode reference page is here: http://genome.ucsc.edu/ENCODE/pubs.html

[J.F.Jiang]

not really. the only information i know is the postion of SNPs, so i want to do so enrichment according to UCSC. But i do not know which TFBS are deserved to be studied, or why does the authour choose thos factors for investigation. Or else if there is any other suggestions>?

Answer 1

[Larry_Parnell]

Why those transcription factors (TFs)? Because they are important and popular and tools are available to test them (antibodies, well characterized binding sites, known/interesting biology, etc.). However, these are by no means the only important TFs. Look at FANTOM and their work - they have some 1000 TFs in mind for the human genome. ENCODE and company would like to map binding sites for all TFs and just started with what you see in the databases.

Maybe for the cell type or biological process that interests you or your research group a handful of other TFs are important and override the need to look at MYC, NFKB1, FOS and others. So, take a step back to the biological question you're addressing and see which resources are available to answer that question. It may turn out that you need to upload into UCSC (as custom tracks) a set of TF data other than what they already have. These new data may come from a study on one of your key TFs because it is just what you need.

If you want all TFBSs, you'll have to wait and hunt. Wait: Not all TFBSs are known for the 1000 or so human TFs. Hunt: Many more are known than are commonly displayed, but you'll have to hunt them down from various resources.

[J.F.Jiang]

thank you for your kind answer, as you say it must come back to the biological question when i start my research. But in fact i do not know whether these SNPs are enriched in which TFBS, so i want to do snp enrichment within all TFBS, but it seems that i can not get all TFBS or which TFBS are more important. So, you mentioned that ENCODE had offered binding site for TFs? could you offer me the website? thank you! or anyother link that i can extract all/most the TFBS(annotation, start-end postion)? Thank you!

[gzr3150]

Hello J.FJiang, I come across the same question with you, can you tell me what is the final approach you use ?

[Larry_Parnell]

OK. Your original question did not say all TFBS. The ENCODE data are easy to find and have been incorporated into the UCSC browser. I don't work with ENCODE data myself and so feel that you should find exactly what it is that your project requires.