Esther Melamed wrote:
Dear Benoit,
Thank you again for your response to my question about chicken-human
orthologs. May I ask you another question on the same issue?
The two Ensembl Gene IDs below map to the Z chromosome in Ensembl and
were present in the file of Z genes that I downloaded in February from
Ensembl's Biomart.
ENSGALG00000006803
ENSGALG00000015433
However, these genes are no longer present in the file that I've
downloaded from Ensembl's Biomart last week. I am using the same query
criteria (filter on Z genes and return Ensembl IDs and Entrez Gene IDs.)
What may be the reason for this discrepancy and is there a way to
download a complete list of all current chicken Z genes?
Dear Esther,
These two genes indeed map the Chicken Z chromosomes. But when you
filter with the option "with EntrezGenes IDs" you get only the gene
ENSGALG00000006803 .
If you dont use this option, you get both genes. The other gene
ENSGALG00000015433 don't have an EntrezGene IDs. When you use this
option you filter on gene having and EntrezGene ID _only_ so if one of
your favorite gene is missing, it's most likely that your gene miss that
external ID.
So, if you want all Z genes, just filter with the chromosome filter, in
that case you'll get all gene on the Z chromosome that are predicted by
Ensembl.
So there is two options: may be in feb you didn't use the "with
EntrezGene IDs" filter, or in the new Ensembl Mart the EntreGene ID
mapping for that particular gene has been lost for some reasons.
Arek could you comment that ?
Hope this helps,
Benoit
Ps: Esther I recommend you to subscribe to the mart-dev mailing list for
this type of questions, and/or contact the ensembl-helpdesk
See:
http://www.ensembl.org/info/about/contact.html
http://www.biomart.org/contact.html
--
Benoit Ballester, PhD
Ensembl Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom
