Filter human transcription factors
1
0
Entering edit mode
10 weeks ago
Chris ▴ 230

Hi Biostars,

I have a list of genes that differential expressed in RNA-seq and would like to filter only transcription factors. Do we have any tools or good way to do this? Thank you so much!

transcription-factor RNA-seq • 630 views
ADD COMMENT
0
Entering edit mode

What have you tried? Have you looked at GO annotations?

ADD REPLY
0
Entering edit mode

Yes, I do GO and GSEA to get pathway. I download the background gene at https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#C3 The things I am quite confuse is there are many different pathway when I use GO, GSEA or using different database such as KEGG or others, so not sure which pathway I should focus on. I found there are many functions that perform pathway analysis such as fgsea(), gseGO(), gseKEGG(), enrichGO()

ADD REPLY
6
Entering edit mode
10 weeks ago

This database has been the best I've found.

ADD COMMENT
1
Entering edit mode

Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resources/motif_clustering

ADD REPLY
0
Entering edit mode

That's a nice resource. Motif redundancy is by far the most frustrating aspect of motif analyses, in my experience. To a degree, we address it by filtering via expression, but it still results in imperfect results.

ADD REPLY
0
Entering edit mode

Thank you so much!

ADD REPLY
0
Entering edit mode

Definitely the best resource. Was also going to recommend this one.

ADD REPLY

Login before adding your answer.

Traffic: 3075 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6