LEGO January 5, 2015

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Agenda

  • Action item from the last call was for me to look up more details for the PHO pathway.

http://go-genkisugi.rhcloud.com/seed/model/gomodel:sgd-536d71c50000004

New Details for the PHO pathway

  • IP7, inositol heptakisphosphate (a metabolite) interacts with Pho81-Pho85-Pho80 complex (this is a constitutive complex). This interaction causes conformational change in Pho81 and this prevents Pho4 from accessing the kinase active site of Pho80-pho85. Hence Pho4 remains unphosphorylated and is able to up regulate transcription of PHO5 (phosphatase) and other genes.
  • In addition to PHO5 (acid phosphatase), PHO4 also activates Pho84 and Pho89 which are high affinity Pi transporters and Spl2 a negative regulator of low affinity transporters (Pho87, Pho90).


Discussion

Modeling

  • Regarding adding IP7, is there an enzyme that makes this metabolite? If yes, then the metabolite should be expressed as the product of that enzyme activity. It is an upstream activity.
  • Kimberley: Can you assign activity to small molecules in LEGO?
    • PT: That would be beyond the scope of GO. Biology controls the making or importing of metabolites by controlling the activities of gene products, genetic control is at the level of genes. SO gene products are the at core. In this case Pho81 detects and binds IP7. So Pho81 should have a IP7 binding function.
  • Suzi- How to connect an upstream process to another LEGO model. In this case, how can we say that there is a separate IP7 biosynthetic process/pathway and put a hook from the IP7 pathway to the PHO pathway?
  • Chris: we can create an instance of the biological process and connect using specific relationships such as upstream_of, provides_input
  • Kimberley: How do we represent the individual/subunit functions of the complex? Do we need to?
  • PaulT added these details post meeting- http://go-genkisugi.rhcloud.com/seed/model/gomodel:sgd-536d71c50000004

technical questions

  • Rama - is there an option to clone a model? Chris: not at the moment. We have to be careful about what cloning should include.
  • Rama- the relaionship text box expects us to start typing and will auto-suggest relationships. Earlier we had an option to select from a pull down list. It is sometimes hard to figure out what to start typing. Is it possible to have the pull-down option again? Chris said that this was by design so we refer to the relationship ontology and pick the right relationship.