What’s the answer? (TF binding data)

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of thecommunity and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s question highlights an issue with transcription factor binding site data. We get a lot of questions about TFBS resources, and they are often varied, scattered, and as you see here–dated. It’s too bad, because there is a ton of good hot new stuff coming out of some of the big-data projects. But without formal curation of that data it’s not that easy to find and use.

Question: Current standard database of TF Position-Weight-Matrices 

What is the current ‘industry standard’ database for human transcription factor PWMs. I used to use JASPAR but the database hasn’t been updated since Oct. 2009 and TRANSFAC has become nearly impossible to download.

Has another database come to popularity in recent years?



So one of the answers was a resource that I hadn’t used before (hPDI), and those are my favorite questions and answers–when I find a new site to check out. Go have a look.

And just after I set up this week’s post, Stephen Turner tweeted this–that gets at some of the ENCODE data I’ve been eager to see wrangled into a useful manner:

RT @genetics_blog: Cscan: Finding Gene Expression Regulators with ENCODE ChIP-Seq Data http://t.co/H13bRfPz #Bioinformatics

Here’s the link for Cscan directly, but go read Stephen’s post for full details. http://www.beaconlab.it/cscan  I feel a tip-of-the-week coming on….