Question: Mapping Custom Agilent Gene Ids To Go Terms
1
gravatar for K. Wyatt Mcmahon
8.1 years ago by
Virginia Bioinformatics Institute, Virginia Tech
K. Wyatt Mcmahon50 wrote:

Hello everyone,

I always come back to BioStar because the help is always useful and quick and the people are always so considerate. I'm sure this experience will be no different.

I am performing an analysis on someone's custom Agilent array design. I am trying to map each /many of the genes on the chip to a GO term (if such an annotation exists). This would be simple if all of the IDs were from one source (ENSEMBL, Genbank, etc). Instead, what I have is a mix of different identifier types for the chip.

I have gone to BioMart and - while hugely powerful - it seems to require that all of the IDs come from the same source. I can separate these out, but I'm wondering if there is a site that can recognize the type of identifier you have and then bring GO terms for you.

I do not have the files used to generate the arrays. I do, however, have the ProbeIDs, SystematicIDs, etc. from the array intensity files.

Thanks in advance for any help you can offer!

Wyatt

agilent gene • 1.8k views
ADD COMMENTlink modified 7.7 years ago by Chris Evelo10.0k • written 8.1 years ago by K. Wyatt Mcmahon50
2
gravatar for Larry_Parnell
8.1 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Couldn't you relate each data source to a standard, unique identifier such as the EntrezGene ID? This would involve querying BioMart several times - once for each data type - but the results, taken together, would get the job done.

Or, because this is a custom array, the person/group who supplied Agilent with the data to build the array may even have this EntrezGene ID info. Perhaps not, and then that becomes a teaching point for them rather then, oh, Bioinformatics will just fix the problem.

ADD COMMENTlink written 8.1 years ago by Larry_Parnell16k

Thanks for your advice, Larry. I'm thinking this is what I'll have to do; I was just wondering if there was some service that everyone knew about that I'm missing out on.

ADD REPLYlink written 8.1 years ago by K. Wyatt Mcmahon50
2
gravatar for Chris Evelo
8.1 years ago by
Chris Evelo10.0k
Maastricht, The Netherlands
Chris Evelo10.0k wrote:

You could try [?]BridgeDB[?] (install locally as a webservice) the standard database provided has Agilent gene ID's (which in fact are contained in ENSEMBL as well, because that is where we have that DB from).

ADD COMMENTlink written 8.1 years ago by Chris Evelo10.0k
1

Ha, no, you are right. You may still want to use BridgeDB but you really need to stack a table with your custom IDs linked to some known ID on top of the database or mapping service you want to use. BridgeDB can do that kind of stacking.

ADD REPLYlink written 8.1 years ago by Chris Evelo10.0k

Thanks for the suggestion, Chris. I actually looked into BridgeDB, and may still go that way. The problem is that this is a custom Agilent array, so it won't have the IDs from this array in BridgeDB.

ADD REPLYlink written 8.1 years ago by K. Wyatt Mcmahon50

Ah! I did not realize that it could do that! I'll look a little more into BridgeDB. Thanks, Chris!

ADD REPLYlink written 8.1 years ago by K. Wyatt Mcmahon50
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