Tools for Discovering Genes Containing a DNA motif
Can anyone recommend tools for generating a list of genes that contain a DNA motif of interest. Ideally, one that provides a summary statistic. I was able to use MEME to identify a motif from several bed files. Now I would like to generate a list of genes with said motif preferably in the promoter region. I used GOMO to get GO terms and that generates gene IDs but these are not in a convenient format. Cheers
• 902 views
•
link
updated
by
jared.andrews07
•
written
by
dk0319 •
•
written
by
dk0319 •
1 answer
I'd probably just use FIMO and intersect the output locations with gene promoters (however you want to define that) via bedtools intersect.
• 0 views
•
link
written
by
jared.andrews07
Log in to answer this question.
More posts like this
-
Identify binding motifs within large super enhancer region
written by mkunika •
-
MEME - minimum of sequence for significative motif result
written by alessandro.alma00 •
-
Use BioMart to get gene names for transcripts with isoform ID (e.g. NM_000014.6)
written by dk0319 •
-
Tools for generating a list of known DNA binding motifs for a DNA binding protein
written by dk0319 •
-
MEME's motifs have an E-vaue too high
written by lspinedaf •
-
Get -400bp to +50bp sequence of gene from gff3 file
written by Biogeek
-
PWM Scan For Toxoplasma gondii
written by mercadocapote •
-
Searching TATA box in the promoters of minus-strand genes
written by chjiao3456 •
-
Motif Seq In Enriched Genes
written by kanwarjag
-
Chipseq Motif In Set Of Genes
written by Honey
