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.
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):
DBD provides downloads and identifiers such as Ensembl gene ID, which are easily converted to Entrez gene ID using BioMart or similar.
Try the UniProt interface e.g.
1,799 results for "transcription factor"AND reviewed:yes AND organism:"Homo sapiens (Human) "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
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.
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.