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 >> > > >
