Identification of Overrepresented Transcription Factor Binding Motifs in the Promoters of a List of DE Genes
1
0
Entering edit mode
JMallory • 0
@jmallory-13488
Last seen 3.5 years ago

Hi, 

I have a list of DE transcripts emerging from an analysis of RNA-seq data. I have mapped these transcripts back to their Ensembl ENSG IDs for submission to the `findMotifs.pl` function in the `HOMER` software suite http://homer.ucsd.edu/homer/microarray/index.html

As described by the link, the goal of `findMotifs.pl` is to extract the promoter region of each gene and look for transcription factor binding motifs that are disproportionately represented in the list of named genes above background levels. As others have described, I am finding this software to be a bit buggy and would much rather use something in Bioconductor that has better documentation/ user community/ version support. Is there any integrated Bioconductor solution to accomplish the analyses described here? 

HOMER Motif Analysis • 697 views
ADD COMMENT
0
Entering edit mode
Ou, Jianhong ★ 1.3k
@ou-jianhong-4539
Last seen 4 months ago
United States

rGADEM package?

ADD COMMENT

Login before adding your answer.

Traffic: 678 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