TF list

Latest list

• File:FANTOM5 Transcriptional regulator list March2012AL.xls (posted on [fantom5:01461])

Old lists

• File:120228-TFlist-NatRevGenet2009Vaquerizas pls VIGG UBC-1.xls (posted on [fantom5:01397])
• File:120210-TFlist-NatRevGenet2009Vaquerizas.xls (see detailed discussion on [fantom5:01320] )

Fantom5 list of transcription factors v02

The FT5 list of human TFs (version 0.2) is uploaded here: Media:tf_list_ft5_v2.tsv.gz

Columns

1.) Uniprot protein ID
2.) Uniprot protein accession
3.) Entrez Gene ID
4.) HGNC gene symbol
5.) Source
6.) Source PMID (if applicable)
7.) TF class (only applicable for TFs taken from Vaquerizas et al., Nat Rev Genet)

Method

A 2009 paper in Nat Rev Genetics (Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM. A census of human transcription factors: function, expression and evolution. Nat Rev Genet 2009 Apr;10(4):252-63.) list a set of 1391 high confidence human curated proteins as TFs. This is based on the proteins having a sequence specific DNA binding domain as well as having some functional annotation with regard to transcription regulation. To adhere to the most widely used standard for protein naming the protein IDs given in this paper were translated into Uniprot IDs. This results in 1337 non-redundant human proteins in Uniprot. Proteins that are listed as TFs in either TRANSFAC (version 11.4) or TfCat (Fulton DL, Sundararajan S, Badis G, Hughes TR, Wasserman WW, Roach JC, Sladek R. TFCat: the curated catalog of mouse and human transcription factors. Genome Biol. 2009;10(3):R29.) but were not already included were added to the list after a manual curation step. 8 proteins from TfCat and 19 proteins from TRANSFAC were added. Were possible the HGNC gene symbols and the Entrez gene IDs of the genes coding for these proteins have been determined. There are 5 proteins that have 2 genes associated with them. 2 proteins have been added after input from a consortium member. 3 proteins added after discussion in the mailing list and futher curation. GABP2_HUMAN was added (as the GABP1 is already present). In total there are 1371 human TFs.

Change history

Changes since the version emailed to FT5 ML on Wed, Oct 19, 2011 (Version 0.0):
Z705C_HUMAN (Q2TAN0) renamed to Z705D_HUMAN (P0CH99)
ZN409_HUMAN (Q9UPU6) deleted (protein record was merged with ZFHX2_HUMAN (Q9C0A1))
Addition of the BPTF_HUMAN, HMGA1_HUMAN, MECP2_HUMAN, GABP2_HUMAN Addition of E2F7 after manual curation

Disclaimer

Functional annotation of proteins is far from complete/correct. This list represents what we believe is a good approximation to a complete list of human TFs based on current data. If you feel strongly about the one or the other protein, please make the required changes and document them in the change history section on this page. Thanks.