[InterMine Dev] "type" in homologue model

rachel at flymine.org rachel at flymine.org
Wed Oct 10 22:20:03 BST 2012


Hi Sierra,

Yes I think this is the correct place to put this information - we used
this field when we loaded panther into FlyMine. We loaded the full name
rather than the codes.

Rachel.





> Hi All-
>
> 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" ?
>
> Thanks,
> Sierra
>
>  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
> duplications occurred.
> 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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