[BioMart Users] Probe Id to Gene symbol

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[BioMart Users] Probe Id to Gene symbol

Nabila Kazmi

I'm trying to convert the probe names of 54k CodeLink Human Whole Genome Bioarray to gene names. Please can you suggest me that is it possible using your services. I explored Biomart but couldn't get success.

I'm looking forward to hearing from you soon.

Best Regards
Dr Nabila Kazmi

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Re: [BioMart Users] Probe Id to Gene symbol

Arek Kasprzyk
Dear Nabila,
We need to bring Rhoda  into these discussions. Rhoda, do you guys have these data in Ensembl and if not, are you planning to include it at some stage?


a




On 26 April 2013 17:04, Nabila Kazmi <[hidden email]> wrote:

I'm trying to convert the probe names of 54k CodeLink Human Whole Genome Bioarray to gene names. Please can you suggest me that is it possible using your services. I explored Biomart but couldn't get success.

I'm looking forward to hearing from you soon.

Best Regards
Dr Nabila Kazmi

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[hidden email]
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Re: [BioMart Users] Probe Id to Gene symbol

Rhoda Kinsella
Hi Nabila and Arek,

Yes we have the CodeLink data in the Ensembl Gene mart. If you go to the release 71 Ensembl BioMart databases at www.ensembl.org//biomart/martview/ you will be able to get the information you need.

First, select Ensembl genes 71 mart and choose the Human dataset. Then in the "GENE" filter section, you can either "Limit to genes with CodeLink probe IDs" or you if you have a list of CodeLink IDs of interest you can search using the "ID list limit" filter (see image1 attached). 

In the Attribute "Features" section you can select the Ensembl Gene ID from the "GENE" attributes, the HGNC ID and HGNC symbol from the "EXTERNAL: External references" section and select the Codelink Probe from the "EXTERNAL: Microarray probes/probesets" section (see image2 attached).

You should be aware that this is not really an "ID converter" as both the Codelink probe IDs and HGNC IDs are mapped to Ensembl genes. So what your query is actually doing is checking whether an input CodeLink ID is mapped to an Ensembl gene ID and then checking if that Ensembl gene ID is also mapped to a HGNC ID. These mappings are done at a particular time point in our release cycle and so if there are recently added HGNC IDs (in the last few weeks) we may not have them. We update these mappings to external resources approximately every 2 to 3 months. 

I really hope that helps, but do feel free to get back to me if you have further questions.
Regards
Rhoda






On 1 May 2013, at 09:32, Arek Kasprzyk <[hidden email]> wrote:

Dear Nabila,
We need to bring Rhoda  into these discussions. Rhoda, do you guys have these data in Ensembl and if not, are you planning to include it at some stage?


a




On 26 April 2013 17:04, Nabila Kazmi <[hidden email]> wrote:

I'm trying to convert the probe names of 54k CodeLink Human Whole Genome Bioarray to gene names. Please can you suggest me that is it possible using your services. I explored Biomart but couldn't get success.

I'm looking forward to hearing from you soon.

Best Regards
Dr Nabila Kazmi

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users





Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD




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