Transcription factor binding site enrichment problem
2
1
Entering edit mode
6.3 years ago

I looked everywhere on the net but I'm unable to answer these questions.

I have a dataset from a microarray experiment (>50 000 probesets, observed throught 4 times and 5 patients)

I made a clustering of the gene expression. I further want to make a gene regulatory inference.

But to do so, I want to incorporate biological prior information. But I need to now :

 

- the potential TFs of each of my clusters (based, for example on a TFBS enrichment analysis)

- the potential targets of each TF in my whole gene selection

 

I would like to find a tool to make both of my taks. I need them to be in R (R-bioconductor).

I read JASPAR with TFBStools may be a good strating point. But I really don't understand how to start : with the list of the genes, with the promoter sequence of the genes (if yes, how can I get these sequences ?)...

Is there something in R like oPOSSUM, that allows to analyse in a direct way a list of genes ?

Thank you in advance, I'm a little lost.

Nicolas

 

 

 

 

transcription factor TFBS bioconductor R • 2.4k views
ADD COMMENT
2
Entering edit mode
6.3 years ago
Zhilong Jia ★ 1.7k

Enrichr

http://amp.pharm.mssm.edu/Enrichr/

ADD COMMENT
1
Entering edit mode
18 months ago
avi.maayan ▴ 10

You can also try:

ChEA3

https://amp.pharm.mssm.edu/ChEA3

ADD COMMENT

Login before adding your answer.

Traffic: 2441 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