@@ -14,8 +14,9 @@ In Ensembl, most genes have a name (e.g. BRCA2) which is assigned from one of th
The current projections which are done are:
Human to chimp,opossum,dog,cow,macaque,chicken,xenopus
Mouse to rat
Human to all mammals (1:1 orthologues only)
Mouse to rat (1:1 orthologues only)
Human to all fish (using 1-many ortholgues as well)
The projection works as follows:
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@@ -25,10 +26,12 @@ The projection works as follows:
Assign "from" gene's name and description to "to" gene
Set status of "to" gene to KNOWN_BY_PROJECTION
If the "to" gene has an existing display xref, this is not overwritten, except in the case where the "to" gene has a name derived from a RefSeq_dna_predicted or RefSeq_peptide_predicted xref, and the "from" gene has a name derived from an HGNC (in the case of human) or MGI (in the case of mouse) xref.
If the "to" gene has an existing display xref, this is not overwritten, except in the case where the "to" gene has a name derived from a RefSeq_dna_predicted or RefSeq_peptide_predicted xref, and the "from" gene has a name derived from an HGNC (in the case of human) or MGI (in the case of mouse) xref.
Note that only homologies of type "ortholog_one2one" and "apparent_ortholog_one2one" are used from Compara. Other types of homology (e.g. one to many) are not used for the projection. This is the case for both the gene name and GO term projection.
As of release 49 (February 2008), only HGNC symbols will be projected from human to the other species. Projections from mouse will continue to use gene names from other sources, e.g. UniProtKB/Swissprot.
GO term projection
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@@ -37,10 +40,12 @@ As with gene names, there are many more GO (Gene Ontology) annotations for human
The following projections are done currently:
Human to mouse, rat, dog, cow, chicken
Mouse to human, rat, dog, cow, chicken
Human to all mammals
Mouse to all mammals
Drosophila to anopheles
All GO term projections use 1:1 orthologues only.
The algorithm for the projection is similar to that for gene names:
