Question: nearby gene and miRNA of non coding RNA
0
gravatar for donny.dw
3.4 years ago by
donny.dw0
donny.dw0 wrote:

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.

non-codings genome • 946 views
ADD COMMENTlink modified 3.3 years ago by Jean-Karim Heriche20k • written 3.4 years ago by donny.dw0
1
gravatar for Chirag Nepal
3.4 years ago by
Chirag Nepal2.2k
Copenhagen
Chirag Nepal2.2k wrote:

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

ADD COMMENTlink written 3.4 years ago by Chirag Nepal2.2k

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

ADD REPLYlink written 3.4 years ago by donny.dw0
0
gravatar for jordi.rodo
3.3 years ago by
jordi.rodo0
jordi.rodo0 wrote:

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

ADD COMMENTlink written 3.3 years ago by jordi.rodo0
0
gravatar for Jean-Karim Heriche
3.3 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche20k wrote:

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).

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Jean-Karim Heriche20k
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