nearby gene and miRNA of non coding RNA

Question

[donny.dw]

I have a non-coding RNA list with positions which is from mouse MTA microarray. What I am planning to do are 1. find their nearby genes, 2. find overlap miRNA.

I am trying to parse related tables/files from UCSC genome browser.

For gene annotation, I downloaded refFlat.txt.gz and knownGene.txt.gz. Which is better? Which one contains all genes annotation of mouse?

For miRNA, which file I should use?

Thanks.

Answer 1

[Chirag Nepal]

Mirna genomic coordinates can be downloaded from this link http://www.mirbase.org/

[donny.dw]

Thanks, but how to map the accession of mirbase to other accession? I can't find the xref file on this database.

Answer 2

[jordi.rodo]

I am also interested in this post. Anyone knows how to retrieve nearby genes? Thanks for the information ;)

Answer 3

[Jean-Karim Heriche]

Ensembl has mapped non-coding RNAs (including miRNAs from miRBase) and they should also have xrefs. You could test whether they have your type of identifiers by running them through the Ensembl BioMart. You can then retrieve the nearby genes using the API (or this may also be possible via BioMart).