This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Transcriptional regulator genes list

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 !!!

genelist transcriptional-regulator
• 2,707 views • link
updated by ZhouK.R. • ZhouK.R. • written by Chirag Nepal Chirag Nepal

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.

• 0 views • link
written by ivivek_ngs ivivek_ngs

1 answer

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.

• 0 views • link
written by ZhouK.R. • ZhouK.R.

Log in to answer this question.

More posts like this