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closeother orthology ressources
Posted by MichaelHan on 08 Jun 2011 at 15:27 GMT
The available comparisons of the C. elegans and human genomes are out of date and suffer from a reliance on early or incomplete drafts of genome sequence information, as well as on earlier, less powerful sequence analysis methods.
http://plosone.org/article/info:doi/10.1371/journal.pone.0020085#article1.body1.sec1.p4
EnsEMBL compara GeneTrees include C.elegans and H.sapiens and are updated every release (3 months). The corresponding C.elegans database is the respective frozen WormBase release. H.sapiens also includes patches from the GRC.
RE: other orthology ressources
danshaye replied to MichaelHan on 08 Jun 2011 at 19:16 GMT
One of the resources we used in our meta-analysis was indeed EnsEMBL Compara. However, as we discuss, even this resource (at least version 57, which was the release at the time of our analysis) was not complete. For example, version 57 of Compara missed human orthologs of several C. elegans genes (e.g, lin-12/Notch, glp-1/Notch and egl-15/FGFR, etc.), whereas the correct orthologs were found by InParanoid and OrthoMCL. This supports our notion that a meta-analysis of several methods was critical for the most comprehensive list. We do note that the most recent release of EnsEMBL Compara (v62) correctly identifies the human orthologs for some of the genes missing in the earlier version (in particular, lin-12, glp-1, egl-15). However, this does not negate our assertion that rather than waiting for refinement to any single resource, the most comprehensive list possible is achieved by the meta-analysis of the various resources available at the time.