[InterMine Dev] "type" in homologue model

Sierra Moxon staylor at cs.uoregon.edu
Tue Oct 9 18:38:33 BST 2012


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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