Question: List Of All Transcription Factors In Human
4
gravatar for dfernan
19 months ago by
dfernan330
United States
dfernan330 wrote:

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!

ADD COMMENTlink written 19 months ago by dfernan330
8
gravatar for Neilfws
19 months ago by
Neilfws41k
Sydney, Australia
Neilfws41k wrote:

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.

ADD COMMENTlink written 19 months ago by Neilfws41k
2
gravatar for cdsouthan
19 months ago by
cdsouthan840
cdsouthan840 wrote:

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

ADD COMMENTlink written 19 months ago by cdsouthan840
1
gravatar for JC
19 months ago by
JC4.8k
Seattle
JC4.8k wrote:

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

ADD COMMENTlink written 19 months ago by JC4.8k

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

ADD REPLYlink written 19 months ago by dfernan330
1
gravatar for Larry_Parnell
19 months ago by
Larry_Parnell15k
Boston, MA USA
Larry_Parnell15k wrote:

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.

ADD COMMENTlink written 19 months ago by Larry_Parnell15k
0
gravatar for Anthony
19 months ago by
Anthony630
Vancouver
Anthony630 wrote:

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.

ADD COMMENTlink written 19 months ago by Anthony630

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

ADD REPLYlink written 18 months ago by cdsouthan840

That's bioinformatics for you :)

ADD REPLYlink written 18 months ago by Neilfws41k

And annotation discordance is most definitely part of the fun

ADD REPLYlink written 18 months ago by cdsouthan840

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.

ADD REPLYlink written 18 months ago by Anthony630

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

ADD REPLYlink written 18 months ago by cdsouthan840
1

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.

ADD REPLYlink written 18 months ago by Anthony630

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).

ADD REPLYlink modified 18 months ago • written 18 months ago by cdsouthan840
0
gravatar for Alex Reynolds
19 months ago by
Alex Reynolds6.2k
Seattle, WA USA
Alex Reynolds6.2k wrote:

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.

ADD COMMENTlink modified 19 months ago • written 19 months ago by Alex Reynolds6.2k

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.

ADD REPLYlink written 19 months ago by Anthony630
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