Question: Overrepresentation Analysis For Microrna Binding Sites In Utrs?
2
gravatar for Michael Imbeault
7.0 years ago by
Michael Imbeault110 wrote:

Hi guys,

I got a list of differentially expressed UTRs (following splicing, data from Affymetrix Exon Arrays) and I would like to see if within those UTRs binding sites for microRNA families are overrepresented. I can't seem to find a software package to do just that however, even if it feels like common workflow.

So before I code myself a solution in bioC, I wanna be sure I'm not reinventing the wheel :D

enrichment utr mirna • 3.4k views
ADD COMMENTlink modified 6.8 years ago by Mns20 • written 7.0 years ago by Michael Imbeault110
4
gravatar for David Quigley
7.0 years ago by
David Quigley10k
San Francisco
David Quigley10k wrote:

Don't know if there is a bioconductor tool already in existence. This isn't my area, but it's an active area of research. Here are some tools to get you started:

MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence

PicTar

TargetScan

You may find the mirBase site useful.

ADD COMMENTlink written 7.0 years ago by David Quigley10k

Thanks, clicking around on mirBase led me to Sylamer (http://www.ebi.ac.uk/enright/sylamer/) which looks like its what I want :) Gonna give it a try and see how it performs.

ADD REPLYlink written 7.0 years ago by Michael Imbeault110
2
gravatar for D. Puthier
7.0 years ago by
D. Puthier320
France/Marseille/Inserm
D. Puthier320 wrote:

Perhaps CORNA (R/BioC).

ADD COMMENTlink written 7.0 years ago by D. Puthier320
2
gravatar for Mns
6.9 years ago by
Mns20
Mns20 wrote:

You could also try mirExTra which seems to be doing what you are asking for. Identifies overrepresented miRNA motifs between two differencially expressed lists of genes

Quoting from its website "The mirExTra algorithm identifies overrepresented six nucleotide long motifs (hexamers) on the 3'UTR sequences of deregulated genes."

ADD COMMENTlink written 6.9 years ago by Mns20
1
gravatar for Casey Bergman
7.0 years ago by
Casey Bergman17k
Athens, GA, USA
Casey Bergman17k wrote:

See list of MicroRNA:UTR software options compiled at wikipedia:

ADD COMMENTlink written 7.0 years ago by Casey Bergman17k
1
gravatar for Fred Fleche
7.0 years ago by
Fred Fleche4.2k
Paris, France
Fred Fleche4.2k wrote:

[?]

http://regrna.mbc.nctu.edu.tw/

Otherwise there is a list of miRNA related tools at the following webpage: http://www.bioinformatics.fr/biology.php?subsection=miRNA

ADD COMMENTlink written 7.0 years ago by Fred Fleche4.2k
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