Question: Gene Id Conversion Tool
4
gravatar for Renee
11.0 years ago by
Renee40
Renee40 wrote:

Hey,

I was using DAVID (http://david.abcc.ncifcrf.gov/conversion.jsp) to do the gene ID conversion, e.g.conversion between Agilent ID, Genebank accession id and Entrez gene ID, but I found the DAVID database is not updated. Does anyone know a better updataed conversion tool to do this job? Thanks!

ADD COMMENTlink modified 10.6 years ago by Dave Bridges0 • written 11.0 years ago by Renee40
3
gravatar for Michael Dondrup
10.6 years ago by
Bergen
Michael Dondrup50 wrote:

BioMart has already been mentioned. It can do much more than ID conversion but it is very useful for conversion purposes, it is regularly updated and you can select different genome builds and all kinds of genomic features. It seems to me that you wish to retrieve GeneIDs linked to Affymetrix IDs. To select these attributes in BioMart: go to the Martview page to start a new BioMart query.

Select attributes on the attribute page: The Ensembl GeneIDs and Transcript IDs are default. Ensembl GeneID and Affy IDs are under the "External" tab. Select your chip there. To limit to those genes which are on the chip, use the Filters->Gene menue. You can limit the genes to those present on various platforms or your favourite set.

There is an URL button in biomart that allows to retrieve a URL for your query and to pass it on to others. Try this example:

BioMart URL URL, that should be a good starting point.

If you are interested in KEGG identifiers (Pathways, Genes), EC-numbers, etc. the

KEGG Identifier page could be handy, because the KEGG ids are not in BioMart as far as I know.

ADD COMMENTlink written 10.6 years ago by Michael Dondrup50
2
gravatar for Mohammed Islaih
10.9 years ago by
Mohammed Islaih20 wrote:

The following link has a list of ID conversion tools:

http://hum-molgen.org/NewsGen/08-2009/000020.html

ADD COMMENTlink written 10.9 years ago by Mohammed Islaih20
2
gravatar for Giovanni M Dall'Olio
10.7 years ago by
Barcelona, Spain
Giovanni M Dall'Olio420 wrote:

You can also do it with the following services:

  • uniprot - Click on 'Id Mapping' from the home page.
  • biomart - choose a database and a version, then put the ids you want to convert under Filters->Id List limit (select the proper input id in the menu), and then the output ids under 'Attributes'. Biomart is a general tool that enables you to extract a lot of different informations from databases - sequences, ontologies, transcripts, homologues - but maybe for converting gene ids is a bit too complex.
  • galaxy - I can't help too much about this here but I am sure it has a function for doing that - and many other things.
ADD COMMENTlink written 10.7 years ago by Giovanni M Dall'Olio420
2
gravatar for Daniel Swan
10.6 years ago by
Daniel Swan20
Oxford, UK
Daniel Swan20 wrote:

http://idconverter.bioinfo.cnio.es/

Is another possible solution to this, although you might find this is not as up to date as you might like either.

ADD COMMENTlink written 10.6 years ago by Daniel Swan20
0
gravatar for István Albert
11.0 years ago by
István Albert ♦♦ 310
University Park
István Albert ♦♦ 310 wrote:

I don't know of a direct solution myself, but this is a topic that may be of interest for the biological data analysis class that I am teaching.

If you specify the organism/genomic builds that you are interested in we may be able to generate a full translation list as an in class example or a homework. I was planning on covering an Affymetrix ID to Genebank example anyhow.

ADD COMMENTlink written 11.0 years ago by István Albert ♦♦ 310
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