List Of Tf And Tfbs From A Non-Model Species

Question

[Nicolas Rosewick]

Hi,

How can I find the TF and TFBS from a non-model species (in my case the cow). Maybe is it possible to infer them with the human TF and TFBS ? My goal is to detect the TF from differentially expressed genes. and maybe the differentially expressed TF regulating differentially genes.

Other related question : how to know which gene encode a TF ?

Thanks a lot,

N.

Answer 1

[Sudeep]

You can try Animal Transcription factor database to find predicted transcription factors and TF genes (not binding genes) including cattle. Otherwise you can use Genomatix suite, you can use their Eldorado Gene2Promoter to retrieve promoter sequences and transcription factor binding site predictions. Although Genomatix is commercial, they allow 7 day trial with access to all the databases if you sign up, which would be more than enough for your purpose I guess. Also if you are using Eldorado, you can also retrieve orthologue human and mouse promoters, but keep in mind that for livestock species, all the promoters available are predicted and there is no experimentally determined promoter, TFBP databases available AFAIK. I hope this answers at least some of your questions.

Answer 2

[Anthony Mathelier]

You can also start from known human and mouse TFs and look for orthologs in cow. TF lists can be found from TFCat (http://www.tfcat.ca/) or the paper by Vaquerizas et al. (http://www.nature.com/nrg/journal/v10/n4/full/nrg2538.html). To retrieve PWMs to predict TFBSs, you can look at the JASPAR CORE vertebrates matrices at http://jaspar.genereg.net/cgi-bin/jaspar_db.pl?rm=browse&db=core&tax_group=vertebrates and restricting predictions to conserved regions.