Transcriptional regulator genes list

Question

[Chirag Nepal]

Hi there,

I have a list of SNV genes of my interest. I want to find how many of these genes are potential transcriptional regulator genes (such TBP, NANOG, Oct4 and so on). Does anybody know a webpage where such information is compiled ?

Thank you !!!

[GouthamAtla]

Like the TFs listed here in FANTOM ? http://fantom.gsc.riken.jp/5/sstar/?title=Data_source&action=edit

[ivivek_ngs]

I think it is not that easy to do that, or might be not feasible directly to find upstream TFs from SNV data or if a SNV is a potential TF. What you can do is create a bed file of the SNV to get chr start end and then use enrichr to find upstream TFs from there but then also it will be a very close call and would rather be false positives for me. What I would suggest is to couple with RNA-Seq data if you have for the samples you obtained SNVs or the phenotype in consideration one can check the public expression data and then to overlap the DEGs with that of SNVs to see if a mutation is corresponding to change in gene expression or rather even the upstream TF analysis from the DEGs giving any TFs as gene names can be crossed with with SNV list from your end. But having a directed approach of TFs from SNV is something which might give a lot of FPs.

Answer 1

[ZhouK.R.]

ChIPBase v2.0 is qualified for this job. In the webpage ( http://rna.sysu.edu.cn/chipbase ), the "Regulator" module can help you retrieve active factors (transcription factors, transcription co-factors and histone modifications) that occurred at upstream or downstream of the TSS of your interested gene.