Question: Transcription Factor Enrichment
17
gravatar for Dave Bridges
3.5 years ago by
Dave Bridges1.0k
Ann Arbor, MI
Dave Bridges1.0k wrote:

What is the recommended (hopefully free) tool for finding enrichment of transcription factor binding sites in a set of promoter sequences?

ADD COMMENTlink modified 14 months ago by Maciej Jończyk310 • written 3.5 years ago by Dave Bridges1.0k
9
gravatar for Alastair Kerr
3.5 years ago by
Alastair Kerr4.5k
The University of Edinburgh, UK
Alastair Kerr4.5k wrote:

Check out the data and tools in the jasper database (Free)

ADD COMMENTlink written 3.5 years ago by Alastair Kerr4.5k

unfortunately not much for nematode

ADD REPLYlink written 21 months ago by Frymor610
6
gravatar for Mary
3.5 years ago by
Mary9.2k
Boston MA area
Mary9.2k wrote:

Depends on what you want to do of course--but you might find some tools in the MEME suite that could help you: http://meme.sdsc.edu/meme/

ADD COMMENTlink written 3.5 years ago by Mary9.2k
5
gravatar for Larry_Parnell
3.5 years ago by
Larry_Parnell15k
Boston, MA USA
Larry_Parnell15k wrote:

A grad student here had this very question at the beginning of her thesis. Like others here, we used TRANSFAC motifs. I would do that again adding JASPAR to the mix. At that time, no tools were known to her. We found two important considerations:

  1. What defines the "promoter" or "gene control region" in human? We settled on 5000 bp of upstream sequence + exon 1 + intron 1 (entire or up to first 1000 bp, can't recall). Why intron 1? Because many gene control elements are found here.

  2. When looking for enrichment, how do you define your set of control genes? By size (given that we took exon 1 and intron 1 data)? By GO categories? By gene position (say the neighboring gene)? This was tough and your solution may be specific to the genes your examining or the question(s) you are after.

The student then ran MAPPER to identify the TRANSFAC motifs.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Larry_Parnell15k
4
gravatar for Will
3.5 years ago by
Will4.0k
Will4.0k wrote:

The PAINT promoter analysis tool is my personal favorite. It will take a list of genes, find the upstream regions automatically, pass them through the free version of TRANSFAC and then compare the enrichment to a background set of genes ... either user provided or from a built-in choice. Everything is quite automated and very customizable.

ADD COMMENTlink written 3.5 years ago by Will4.0k
4
gravatar for Ian
3.5 years ago by
Ian3.3k
University of Manchester, UK
Ian3.3k wrote:

You could try PSCAN http://159.149.109.9/pscan/ it uses TFBS from both TRANSFAC and JASPAR.

ADD COMMENTlink written 3.5 years ago by Ian3.3k
3
gravatar for Khader Shameer
3.5 years ago by
Rochester, MN
Khader Shameer14k wrote:

I would suggest you to may customize your favorite GO enrichment tool in a way that the background list of genes will only represent the TFs or genes with TF related terms and perform the enrichment calculation. I tried this one for a small analysis.

Other option is to use a published method like Modulator inference by network dynamics (MINDy) . Disclaimer: I have not tried MINDy myself.

ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by Khader Shameer14k
2
gravatar for Cassj
3.5 years ago by
Cassj1.1k
London
Cassj1.1k wrote:

Maybe RSAT? It seems to have a fairly broad collection of useful motif and CRM building and scanning tools, although I haven't used them myself yet so I can't tell you anything much about them. Web site/services are free but I think you have to register by post(?!) to install tools locally. http://rsat.ulb.ac.be/rsat/

ADD COMMENTlink written 3.5 years ago by Cassj1.1k
2
gravatar for Fiamh
3.5 years ago by
Fiamh190
Boston, MA
Fiamh190 wrote:

I'd second MEME as a conservative approach. Try to see which patterns are stable over a range of promoter sizes, promoter subsets and cutoffs. Once you have those switch to TOMTOM (part of the MEME suite) to map it to JASPER or TRANSFAC matrices.

ADD COMMENTlink written 3.5 years ago by Fiamh190
2
gravatar for Fiamh
3.5 years ago by
Fiamh190
Boston, MA
Fiamh190 wrote:

That's actually one major difference between the various tools -- Dave, do you have a list of genes or promoter sequences? Many tools expect a list of genes because they have their own concept of what a promoter is. If you have CAGE or RNA-Seq data and would like to define which promoter you are interested in half of the existing systems won't be of use to you. Likewise, if you are working with a species not supported by the system you'd be out of luck.

ADD COMMENTlink written 3.5 years ago by Fiamh190

i have genes (but i used biomart to get my own promoter sequences)

ADD REPLYlink written 3.5 years ago by Dave Bridges1.0k

In that case a number of systems such as CisRed won't make sense to use as they have their own, fixed definition of start sites and promoters. The second question would be just how many promoters do you have. If it's just a few you probably have to revert to systems that use phylogenetic footprinting to increase your chances of finding functional binding sites.

ADD REPLYlink written 3.5 years ago by Fiamh190
2
gravatar for Maciej Jończyk
14 months ago by
Maciej Jończyk310 wrote:

For people working with plants the ELEMENT could be useful.
It searches not only for known motifs but also for enriched words.

ADD COMMENTlink written 14 months ago by Maciej Jończyk310
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