[biomart-users] Affy MoGene 2.0 identifiers in Biomart

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[biomart-users] Affy MoGene 2.0 identifiers in Biomart

Javier
Dear list,
I'm trying to obtain from Biomart, those Affy IDs related to miRNA. It seems quite straightforward from www.ensembl.org/biomart. However, from the attributes section and taking into account my set of microarray data (MoGene ST 2.0), I can only select related attributes such as Affy MoGene 1_0 probeset or Affy MoGene2_1 probeset. There is no attribute for Affy MoGene 2.0, why?

I've checked previous releases of Biomart and no attribute for Affy MoGene 2.0  is found.

Any tips?
Thanks,
Javier

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Re: [biomart-users] Affy MoGene 2.0 identifiers in Biomart

Thomas Maurel
Dear Javier,

I am afraid we don’t have the MoGene 2.0 data in the Ensembl Gene mart e!82 at the moment. I have the feeling that the MoGene 2.1 set is more recent than the 2.0 but I will check with my colleagues which are taking care of importing the probe data and mapping them to the Ensembl data.

HTH,
Thomas
On 7 Oct 2015, at 15:10, Javier <[hidden email]> wrote:

Dear list,
I'm trying to obtain from Biomart, those Affy IDs related to miRNA. It seems quite straightforward from www.ensembl.org/biomart. However, from the attributes section and taking into account my set of microarray data (MoGene ST 2.0), I can only select related attributes such as Affy MoGene 1_0 probeset or Affy MoGene2_1 probeset. There is no attribute for Affy MoGene 2.0, why?

I've checked previous releases of Biomart and no attribute for Affy MoGene 2.0  is found.

Any tips?
Thanks,
Javier


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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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Re: [biomart-users] Affy MoGene 2.0 identifiers in Biomart

Javier
Thanks Thomas,

It sounds strange to me, because MoGene 1.0 is available in the Ensemble Gene Biomart v.82. Maybe, there is no difference between MoGene 2.1 and Mogene 2.0.....

Thanks,
Javier


El miércoles, 7 de octubre de 2015, 16:38:15 (UTC+2), Thomas Maurel escribió:
Dear Javier,

I am afraid we don’t have the MoGene 2.0 data in the Ensembl Gene mart e!82 at the moment. I have the feeling that the MoGene 2.1 set is more recent than the 2.0 but I will check with my colleagues which are taking care of importing the probe data and mapping them to the Ensembl data.

HTH,
Thomas
On 7 Oct 2015, at 15:10, Javier <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="TqJpg3uuBwAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">jpfl...@...> wrote:

Dear list,
I'm trying to obtain from Biomart, those Affy IDs related to miRNA. It seems quite straightforward from <a href="http://www.ensembl.org/biomart" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%2Fbiomart\46sa\75D\46sntz\0751\46usg\75AFQjCNGGo-R0j4dWVbu-wzqP-fllPzBNPA&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%2Fbiomart\46sa\75D\46sntz\0751\46usg\75AFQjCNGGo-R0j4dWVbu-wzqP-fllPzBNPA&#39;;return true;">www.ensembl.org/biomart. However, from the attributes section and taking into account my set of microarray data (MoGene ST 2.0), I can only select related attributes such as Affy MoGene 1_0 probeset or Affy MoGene2_1 probeset. There is no attribute for Affy MoGene 2.0, why?

I've checked previous releases of Biomart and no attribute for Affy MoGene 2.0  is found.

Any tips?
Thanks,
Javier


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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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Re: [biomart-users] Affy MoGene 2.0 identifiers in Biomart

Thomas Maurel
Dear Javier,

From what I’ve gathered from my colleagues, we have the MoGene 1.0 data available in Ensembl since release 50 (July 2008). In October 2014, we investigated the addition of the Mogene 2.0 set into Ensembl but the Mogene 2.1 set was added instead.
We are pretty confident that exactly the same probes are on the 2.0 and 2.1 arrays, it’s just that the physical arrays have changed (http://media.affymetrix.com/support/technical/datasheets/mouse_gene_array_datasheet.pdf) but this is pretty hard to prove though, as affymetrix only provide annotations for 2.1. This seems to be backed up by the answer that you had on the BioConductor forum: https://support.bioconductor.org/p/73059/.

Hope this helps,
Regards,
Thomas 
On 8 Oct 2015, at 09:03, Javier <[hidden email]> wrote:

Thanks Thomas,

It sounds strange to me, because MoGene 1.0 is available in the Ensemble Gene Biomart v.82. Maybe, there is no difference between MoGene 2.1 and Mogene 2.0.....

Thanks,
Javier


El miércoles, 7 de octubre de 2015, 16:38:15 (UTC+2), Thomas Maurel escribió:
Dear Javier,

I am afraid we don’t have the MoGene 2.0 data in the Ensembl Gene mart e!82 at the moment. I have the feeling that the MoGene 2.1 set is more recent than the 2.0 but I will check with my colleagues which are taking care of importing the probe data and mapping them to the Ensembl data.

HTH,
Thomas
On 7 Oct 2015, at 15:10, Javier <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="TqJpg3uuBwAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;" class="">jpfl...@...> wrote:

Dear list,
I'm trying to obtain from Biomart, those Affy IDs related to miRNA. It seems quite straightforward from <a href="http://www.ensembl.org/biomart" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%2Fbiomart\46sa\75D\46sntz\0751\46usg\75AFQjCNGGo-R0j4dWVbu-wzqP-fllPzBNPA';return true;" onclick="this.href='http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org%2Fbiomart\46sa\75D\46sntz\0751\46usg\75AFQjCNGGo-R0j4dWVbu-wzqP-fllPzBNPA';return true;" class="">www.ensembl.org/biomart. However, from the attributes section and taking into account my set of microarray data (MoGene ST 2.0), I can only select related attributes such as Affy MoGene 1_0 probeset or Affy MoGene2_1 probeset. There is no attribute for Affy MoGene 2.0, why?

I've checked previous releases of Biomart and no attribute for Affy MoGene 2.0  is found.

Any tips?
Thanks,
Javier


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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom


--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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