[InterMine Dev] "type" in homologue model
staylor at cs.uoregon.edu
Tue Oct 9 18:38:33 BST 2012
The panther ortho data set has a field that helps identify how closely
related an ortholog is. It is different from an evidence code, and
consists of the following values: "LDO, O, ND" (see description below).
I see a "type" column in the homologue model, but flymine seems to use
this to distinguish between "paralogues" and "orthologues." Any
objections to cross-purposing this column to include "LDO,O,ND" ?
From Panther site:
“LDO” means least diverged ortholog, while other, more diverged
orthologs (if any) are marked “O”. Paralogs are marked “P”.
For orthologs, the species column gives the modern-day species in
which the ortholog is found. For paralogs, the species column gives
the two speciation events between which the duplication occurred that
generated the paralogous genes. “ND” means “not determined”. Thus
different paralogs can be distinguished by how long ago the relevant
Orthologs are genes that can be traced to the same gene in the genome
of their most recent common ancestor species. Paralogs are genes that
are traced to related, but distinct, genes in the genome of their most
recent common ancestor species.
The LDO can be loosely interpreted as the most nearly “equivalent”
gene in another organism. If there were no gene duplication events
following the speciation event that separated two species, there is
only a single ortholog in each genome and they are therefore marked as
“LDO.” If there was a gene duplication event following speciation,
there may be more than one ortholog and the least diverged ortholog
pair is marked “LDO,” while other ortholog pairs are marked “O.”
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