Overrepresentation Analysis For Microrna Binding Sites In Utrs?

Question

[Michael Imbeault]

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

Answer 1

[David Quigley]

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.

[Michael Imbeault]

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.

Answer 2

[D. Puthier]

Perhaps CORNA (R/BioC).

Answer 3

[Mns]

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."

Answer 4

[Casey Bergman]

See list of MicroRNA:UTR software options compiled at wikipedia

Answer 5

[Fred Fleche]

[?]

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