I have differentially expressed genes from my microarray data and i would like to know if there are any knowledge sources/tools with the collection of all known Transcription factors from Mouse/Human/Vertebrates that would help me to fish out the genes from my list which are transcription factors.
Have a look at the work I am involved in; We are trying to solve this question right now, because it is not only you who has this problem. For immediate "aid", this database is a collection of curated human/mouse/rat TFs: http://norstore-trd-bio0.hpc.ntnu.no/ Everything still in its infancy, but I hope it is a start you can use.
Thanks Florian for the reply.
I found a previous post for the same question:
https://www.researchgate.net/post/I_have_a_list_of_genes_and_I_need_to_know_which_of_them_is_a_transcription_factor_Can_anyone_suggest_a_tool?exp_tc=tprc
and now going through the suggestions and will let you know after trying all the possible ways.
Just two well known databases:
Transfac - http://www.gene-regulation.com/pub/databases.html
and
JASPAR - http://jaspar.genereg.net/
Thanks Kun Sun for the link but unfortunately i am unable to download the file for Mouse TFs.
@Kun: Yes, that hits the "nail on the head" for the issue we are trying to solve; Even more, some TFs recorded in existing TF resources or the ENCODE 100 (or, well, 96, AFAIR) TF collection are not "strict" TFs in the sense that while they are involved in gene regulation, they do not directly bind DNA or at least are not known (with any experimental proof) to do so. This shortcoming provided us with the incentive to kick-off TFCheckPoint that we are now trying to evolve in collaboration with the GOA and IMEX DBs, but as already said, we are pretty much in the infancy of all this.
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