Current Standard Database Of Tf Position-Weight-Matrices

Question

[Will]

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?

Thanks -Will

Answer 1

[Chris Evelo]

When I read your question my first thoughts were "What the #? What is wrong with JASPAR?" I checked and you are right, there have been no updates since 2009. Since JASPAR is a core resource that integrates the results of enormous amounts of work (both wetlab and drylab) I was quite disappointed about that and contacted the JASPAR team directly. I did receive an answer within a day stating that they plan "a quite massive update with new ChIP-seq data", which "will be a 10% increase of JASPAR core or more." So it is at least clear that the JASPAR team is still alive and I hope we soon see some result showing they are still kicking.

[Will]

Awesome, thanks for the leg-work, its great to hear that they're coming back. I was also surprised and disappointed when I went onto their database and found that the download I had from 2 years ago is identical to current version.

[Anthony Mathelier]

Hello every one, I am part of the Wasserman lab. Thank you for your interest in JASPAR. We are currently working on the new update of JASPAR which will be a massive update of the profiles thanks to ChIP-seq data and including new features.

[Chris Evelo]

Thanks Anthony! Great that you take the trouble to come tell yourself. Any idea when that is due?

[Anthony Mathelier]

We are pushing hard to make it happen as soon as possible, hoping to publish in the coming months.

[Anthony Mathelier]

Our JASPAR2014 manuscript has been accepted with minor revisions for the next issue of NAR database so it should be out soon.

[R. Taylor Raborn]

Hi Will- I had a similar issue to yours and was happy to discover the news about the JASPAR updates- thanks Anthony et al! Here's the link to the JASPAR2014 paper which is now in print: http://www.ncbi.nlm.nih.gov/pubmed/24194598

Answer 2

[Gjain]

Hi Will,

You can look at Human Protein-DNA Interactome (hPDI)

The hPDI database holds experimental protein-DNA interaction data for humans identified by protein microarray assays. The current release of hPDI contains 17,718 preferable DNA binding sequences for 1013 human DNA-binding proteins.

You can use their web tool or download the PWMs from here.

I hope this helps.

Answer 3

[Mary]

I just happened to be looking at another paper where they were describing what they used:

A dataset of 1,213 PWMs corresponding to mouse or human transcription factors was obtained from various sources (TRANSFAC 10.2, JASPAR 2010, UNIPROBE).

From TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks http://www.biomedcentral.com/1471-2105/13/19 BMC Bioinformatics 2012, 13:19 doi:10.1186/1471-2105-13-19

And UniProbe was new to me. So maybe others aren't aware of it either. But maybe you'd want to look. I don't know anything about it yet (now I'm reading up) but you might find some utility there.

Here's UniPROBE: http://thebrain.bwh.harvard.edu/uniprobe/

[Will]

Thanks for the link ... but looking at the data, they actually only have 4(!) human binding motifs. Not sure if that's just a weird database error (seeing how all searches return a database error) or if their focus is elsewhere.