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#15 make ECO:0000201 a child of ECO:0000080?

open
nobody
None
5
2011-08-31
2011-08-31
alan_bridge
No

Hi ECO

would you consider making ECO:0000201 sequence orthology evidence a child of ECO:0000080 phylogenetic evidence?

The reason this might be appropriate is that orthology is determined relative to a speciation event on a phylogenetic tree. Orthologs in two species arise from a common ancestral gene in a shared ancestor - i.e. they arise by speciation, not duplication. Orthology is therefore a specific type of inference drawn from phylogenetic evidence.

Would you also take a look at the definition? Some of the types of evidence cited in ECO:0000201 like "coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors." do not really allow you to conclude that two proteins are orthologous. Orthology is really "just" an evolutionary relationship. Orthologs might have differing expression patterns, different functions, different cross reactivity, subcellular locations, substrate specificities and so on. These other types of evidence might sometimes be used to support an inference of orthology, but only when the inference by phylogenetic means is difficult. People might say "on a phylogenetic tree it's not really sure, but as the proteins do the same job, I think they are probably orthologs". Therefore you might sometimes see an annotation "this protein X is an ortholog of protein Y" linked to an ECO code that has nothing to do with phylogeny....

Best Regards, Alan

Discussion

  • Marcus

    Marcus - 2011-08-31

    Hello Alan,

    You raise some good points here, which we will keep in mind as we rewrite the definition. Typically, when I rewrite a definition, I strive to make it succinct and Aristotelian (this term has not been rewritten yet). Most of the items that you discuss will go into the comments field as the definition is reworked. If you have a suggested definition, I would be grateful to hear it. I think your comments on parentage are helpful, and we will consider this.

    Marcus

     
  • alan_bridge

    alan_bridge - 2011-09-01

    Hi Marcus

    how about something like

    Orthology is a specific type of homology relationship. Orthologs in different species originated by vertical descent from a single gene of the last common ancestor. Given that orthology is defined relative to a speciation event, orthology is normally inferred using phylogenetic methods. Orthologs often, but not always, have similar functions.

    Alan

     

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