Hi Leandro,
its indeed a very good resource. Could you send us the working URL when
you are happy with the data integrity and have certain degree of
confidence that you would be able to maintain it for BioMart user community.
Thanks
Syed
On 25/10/2010 18:21, Leandro Hermida wrote:
Hi Dong,
My NetAffx mart can output a table like this (below), which can give
you all the orthologs between all human, rat and mouse chips with the
correct filters applied. But isn't this pairwise too? I don't know
why that would be a problem, you still get a table for each probe set
on one of the chips *all* the orthologs on the other chips.
-Leandro
Probe Set ID Chip Type Ortholog Probe Set ID Ortholog Chip Type
1007_s_at HG-U133A_2 1584561_at Canine
1007_s_at HG-U133A_2 1598717_at Canine
1007_s_at HG-U133A_2 cfa.18678.1.s1_s_at Canine_2
1007_s_at HG-U133A_2 cfa.7473.1.a1_at Canine_2
1007_s_at HG-U133A_2 cfaaffx.1636.1.s1_s_at Canine_2
1007_s_at HG-U133A_2 l57509_s_at Mu11KsubA
1007_s_at HG-U133A_2 1415797_at MOE430A
1007_s_at HG-U133A_2 1415797_at Mouse430_2
1007_s_at HG-U133A_2 1415797_at Mouse430A_2
1007_s_at HG-U133A_2 1415797_at HT_MG-430A
1007_s_at HG-U133A_2 1415798_at MOE430A
1007_s_at HG-U133A_2 1415798_at Mouse430_2
1007_s_at HG-U133A_2 1415798_at Mouse430A_2
1007_s_at HG-U133A_2 1415798_at HT_MG-430A
1007_s_at HG-U133A_2 1435820_x_at MOE430A
1007_s_at HG-U133A_2 1435820_x_at Mouse430_2
1007_s_at HG-U133A_2 1435820_x_at Mouse430A_2
1007_s_at HG-U133A_2 1435820_x_at HT_MG-430A
1007_s_at HG-U133A_2 1437619_x_at MOE430A
1007_s_at HG-U133A_2 1437619_x_at Mouse430_2
1007_s_at HG-U133A_2 1437619_x_at Mouse430A_2
1007_s_at HG-U133A_2 1437619_x_at HT_MG-430A
1007_s_at HG-U133A_2 1438367_x_at MOE430A
1007_s_at HG-U133A_2 1438367_x_at Mouse430_2
1007_s_at HG-U133A_2 1438367_x_at Mouse430A_2
1007_s_at HG-U133A_2 1438367_x_at HT_MG-430A
1007_s_at HG-U133A_2 1439382_x_at MOE430A
1007_s_at HG-U133A_2 1439382_x_at Mouse430_2
1007_s_at HG-U133A_2 1439382_x_at Mouse430A_2
1007_s_at HG-U133A_2 1439382_x_at HT_MG-430A
1007_s_at HG-U133A_2 1456226_x_at MOE430A
1007_s_at HG-U133A_2 1456226_x_at Mouse430_2
1007_s_at HG-U133A_2 1456226_x_at Mouse430A_2
1007_s_at HG-U133A_2 1456226_x_at HT_MG-430A
1007_s_at HG-U133A_2 100155_at MG_U74Av2
1007_s_at HG-U133A_2 1415797_pm_at HT_MG-430_PM
1007_s_at HG-U133A_2 1415798_pm_at HT_MG-430_PM
1007_s_at HG-U133A_2 1435820_pm_x_at HT_MG-430_PM
1007_s_at HG-U133A_2 1437619_pm_x_at HT_MG-430_PM
1007_s_at HG-U133A_2 1438367_pm_x_at HT_MG-430_PM
1007_s_at HG-U133A_2 1439382_pm_x_at HT_MG-430_PM
1007_s_at HG-U133A_2 1456226_pm_x_at HT_MG-430_PM
1007_s_at HG-U133A_2 tc16141_s_at Mu19KsubA
1007_s_at HG-U133A_2 tc23346_s_at Mu19KsubA
1007_s_at HG-U133A_2 1459990_at MOE430A
1007_s_at HG-U133A_2 1459990_at Mouse430_2
1007_s_at HG-U133A_2 1459990_at Mouse430A_2
1007_s_at HG-U133A_2 1459990_at HT_MG-430A
1007_s_at HG-U133A_2 1459990_pm_at HT_MG-430_PM
1007_s_at HG-U133A_2 1370216_at RAE230A
... ... ... ...
On Mon, Oct 25, 2010 at 6:55 PM,<don...@caltech.edu> wrote:
Hi Leandro,
I am very interested in it. By using EnsMart, I can only get pairwise
orthologs, but I want to find all orthologs among homo, Mouse and rat, do
you know there is any easy way to get them?
Thanks,
Dong
Hi BioMart community,
I don't know if this would be of interest to people, a long while ago
I made a single Perl script which would automatically download all the
annot and ortholog NetAffx files from Affymetrix, parse and process
all the annotations and create a BioMart mart out of it in one go. I
don't know if the BioMart Central Portal or others would be interested
in this? I would be more than happy to release this to the community
best,
Leandro
