List Of All Transcription Factors In Human

Question

[dfernan]

Hi,

Is there any list of all transcription factors in humans and their respective ensemble gene id?

I have been trying to find one but haven't been able to do so. In this paper http://www.sciencedirect.com/science/article/pii/S0959440X04000788 they mention that there are around 2,600 proteins that function as TFs but they do not provide a table or a list as supplementary.

I am curious to know if someone has run into such table.

Thanks!

[komusica]

http://www.tfcheckpoint.org/ manually curated list of mammalian transcription factors, including specific dbTFs

Answer 1

[Neilfws]

Perhaps a better starting point than GO accessions would be a TF database. A couple of examples (easily found via web search for "transcription factor" + database):

• AnimalTFDB - 1544 entries for H.sapiens
• DBD - 2886 (predicted) entries for H.sapiens

DBD provides downloads and identifiers such as Ensembl gene ID, which are easily converted to Entrez gene ID using BioMart or similar.

Answer 2

[cdsouthan]

Try the UniProt interface e.g.

1,799 results for "transcription factor"AND reviewed:yes AND organism:"Homo sapiens (Human) [9606]"in UniProtKB

These are name matches so its not completely clean as you get some co-factors. You could pick out the InterPro domains and or look at the GO terms that fit and make a union

You can then use the "Customise results" to get the Ensembl ID or any other X-ref

Answer 3

[JC]

You can use BioMart (http://www.ensembl.org/biomart/) and filter by GO

[dfernan]

Thanks. What'd be the GO term for Transcription factor? I tried GO:0003700 and seems to work...

[JC]

check the list in AmiGO: http://amigo.geneontology.org/cgi-bin/amigo/search.cgi?search_query=transcription+factor&search_constraint=term&action=new-search

Answer 4

[Larry_Parnell]

Don't overlook the utility of the list of TFs used by the FANTOM consortium. See the suppl file for the paper by Ravasi et al (2010) Cell 140:744-752.

Answer 5

[Anthony Mathelier]

You can have a look at TFCat (http://www.tfcat.ca/, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2691000/) to get a list of TFs with their entrez gene IDs. There is also the paper from Vacquerizas et al. (http://www.ncbi.nlm.nih.gov/pubmed/19274049) where you can get a list of TFs.

[cdsouthan]

To say the numbers we are digging out are discordant is putting it mildly

DBD - 2886 (predicted) entries for H.sapiens Babu et al 2,600 Fantom set 1988 UniProt 1,799 AnimalTFDB - 1544 entries for H.sapiens Vaquerizas et al 1,391

[Neilfws]

That's bioinformatics for you :)

[cdsouthan]

And annotation discordance is most definitely part of the fun

[Anthony Mathelier]

Some people are less stringent in calling a protein a TF. I currently worked on the curation of a list of human TFs (not published yet) and we are reaching around 1500 TFs when asking for experimental validation of DNA-binding AND effect on gene expression.

[cdsouthan]

Will you send those two annotation tags for that protein set over to UniProt when you are done ?

[Anthony Mathelier]

I am far from the leader on this project which is part of the new FANTOM5 but I do not think it is supposed to be linked to UniProt (as far as I know). But the list of TFs will be available when the paper will be published (it is close to submission now). Will let you know if you want.

[cdsouthan]

Thanks, but please tell your esteemed project leader, who almost certainly knows some UniProt folk anyway, that your hard-grafted expert annotation belongs exactly in the UniProt x-ref lines (or keyword field depending on how best to slot it in). You then don't need to send me anything because I can just query the clean set out (but if your paper is not OA I would certainly appreciate a PDF).

[liux.bio]

Hello, have your paper been published? If so, could you give me a link? I want to gain the TFs list. Thanks!

[dvanic]

See human and mouse.

[Dave Gerrard]

dvanic. I think this resource is now worthy as a separate answer to the original question.

Answer 6

[Alex Reynolds]

TRANSFAC and JASPAR CORE are curated TF databases, which include human transcription factors. The second database is free and aims at non-redundancy, while the first is not free and is redundant. Both databases can include accession information for recovering protein names from external sites.

[Anthony Mathelier]

JASPAR is a database of TFs for which we have motifs. TFCat has also been developped by our lab and aimed at giving a curated catalog of mouse and human transcription factors.