Where Can I Find A List Of Human Tfs?

Question

[Kate]

I'm new to bioinformatics, and I need to determine which genes in my list of Entrez GeneIDs are transcription factors. It seems like the simplest way to do this would be to find a list of human transcription factors, convert if needed, and then check if my genes are in the list. But I can't find a list of human transcription factors! I would imagine that it's out there somewhere...can you help me find one? Or explain why there isn't one?

Thanks, Kate

Answer 1

[Larry_Parnell]

I would also use the information from FANTOM, the large international consortium that is mapping all human TFs and the genes they regulate. See Table S1, the list of human TFs used by Ravasi (2010 Cell 140: 744-752) to describe transcription networks and interacting pairs. They have listed over 1970 human genes.

[Kate]

I'm sorry avilella, with this list I found 20% more transcription factors in my list of genes. I also like the fact that I didn't have to convert anything, since the list included Entrez GeneIDs for every TF. Thanks Larry_Parnell!

[Larry_Parnell]

Kate - thank you for the good word. You may find that a combined list is quite valuable where genes present in both lists are of higher confidence or value as you go forward than those only on one list. Nonetheless, those TFs on one list are important. In other words, you keep track of doubly and singly listed TFs.

[Kate]

That's a good point. Thanks for the tip!

[Giovanni M Dall'Olio]

A list of transcription factors produced by FANTOM5 is also available in their SSTAR browser: http://fantom.gsc.riken.jp/5/sstar/Browse_Transcription_Factors_hg19

Answer 2

[2184687-1231-83-]

You may want to have a look at the list in this paper by JM Vaquerizas et al.:
http://www.ncbi.nlm.nih.gov/pubmed/19274049

[Kate]

Thank you avilella! I converted the ENSEMBL IDs from their supplementary table 3 to Entrez Gene IDs using DAVID, and I was able to find a large number of TFs in my data.