Tf And Gene(S) Regulated By Them

Question

[Dataminer]

Hi!

Is there any database which can give you information about the genes regulated by transcription factors?

Or

What could be a better way to extract such information.....Any suggestions

Thank you,

[Chris Evelo]

Please also check this question.

[Khader Shameer]

@SNPminer: Are you looking for information on transcription factor (protein that bind to DNA which may initiate/regulate/repress expression of a distal/proximal gene) and it's target gene (distal/proximal gene regulated by the binding of TFs)? Then see this discussion.

[Dataminer]

Thank's for the link. Shameer's answer stands out again (I am not surprised).

[Dataminer]

To all, kindly see the link given by Chris, and look for the answer given by Khader Shameer. :)

[fcaramia]

hey! What did you end up using? I'm looking for a DB of known regulators of genes.

Answer 1

[Bert Overduin]

Hello,

In Ensembl we do a so-called "regulatory build" for human and mouse. In short, ChIP-seq data (DNaseI sensitivity, CTCF and TF binding, histone modifications and RNA Pol binding) from different cell lines / types are analysed to come up with a "best guess" set of regulatory features. For a detailed description of the regulatory build, please see http://www.ensembl.org/info/docs/funcgen/index.html.

In addition, for each transcription factor (TF) which has both a ChIP-seq data set in the functional genomics database and a publicly available position weight matrix (PWM) we also annotate the position of putative TF binding sites within the peaks called using the ChIP-seq reads. The PWMs are taken from the JASPAR database. See also http://www.ensembl.info/blog/2011/05/18/transcription-factor-binding-sites-in-ensembl/.

Regulatory features are shown on several views in the Ensembl browser and can also be retrieved using the Perl Funcgen API and BioMart.

Note though that we don't make any functional associations between genes and potential regulatory features.

Hope this helps.

Answer 2

[Ian]

I am not sure there is one, or at least a comprehensive one. The problem is it is difficult to say whether a gene is regulated by a particular transcription factor without lab testing. A heuristic with ChIP-seq data is to find the closest gene (by closest edge or TSS). But just because it is close does not guarantee functional association. Genes can be regulated by enhancers that are 100s of kb away from the TSS, even on the other side of another flanking gene!

If you are happy with this woolliness, you can get ChIP-seq data from ENCODE (UCSC), GEO, ArrayExpress and use GALAXY for example to associate genes to binding regions.

Answer 3

[Gjain]

you can use Transfaq or Jaspar databases (http://jaspar.cgb.ki.se/) which uses pfm and pwms to get the relevant information and use those models for further analysis...

[Lyco]

The real name is TRANSFAC not TRANSFAQ, and it is a commercial database. JASPAR is free and strives to be an open TRANSFAC replacement, but to my knowledge there is no information on which genes are regulated by what transcription factors. Rather, there is an (incomplete) list of transcription factors with some PSWMs for their binding site. I can't compare the quality of TRANSFAC and JASPAR matrices because of the TRANSFAC's $$$-tag

[Dataminer]

could you please explain a bit more as to how the matrice information can be manipulated.

[Lyco]

i9 the real name is TRANSFAC not TRANSFAQ, and it is a commercial database. JASPAR is free and strives to be an open TRANSFAC replacement, but to my knowledge there is no information on which genes are regulated by what transcription factors. Rather, there is an (incomplete) list of transcription factors with some PSWMs for their binding site. I can't compare the quality of TRANSFAC and JASPAR matrices because of the TRANSFAC's $$$-tag.

[Dataminer]

well by this approach you can just get the motifs (which could also be false).

[Chris Evelo]

Anything can be false but the JASPAR effort clearly aims at getting high quality motifs. When I asked the JASPAR team to compare JASPAR and Transfac they simply said (we have less, but what we have is better). An open data source that contains inferred and confirmed (by ChIP) motifs per gene would be a great idea. I guess somebody should just start this.

[Dataminer]

@ Dr.Evelo: True anything can be false, but the question is, " A database which houses transcription factor and the genes regulated by them (probably it will contain experimentally proven ones either by ChIP-ChIP or ChIP seq)".

[Gjain]

sorry about the typo.

Answer 4

[Quariel]

You can use RegulonDB http://regulondb.ccg.unam.mx/ but this database contains only the information for E. coli K-12.

=)

[Dataminer]

I am looking for Human.... anyway thanks