List Of All Transcription Factors In Human
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9.1 years ago
dfernan ▴ 710

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!

transcription ensembl genes • 45k views
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http://www.tfcheckpoint.org/ manually curated list of mammalian transcription factors, including specific dbTFs

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9.1 years ago
Neilfws 49k

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.

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9.1 years ago
cdsouthan ★ 1.9k

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

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JC 12k

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

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

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9.1 years ago

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.

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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.

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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

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That's bioinformatics for you :)

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And annotation discordance is most definitely part of the fun

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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.

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

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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.

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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).

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

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See human and mouse.

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

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9.1 years ago

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.

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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.