Ontology meeting 2012-02-15: Difference between revisions

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MINUTES: BECKY
===Discussion item I===
===Discussion item I===
Update on CHEBI xps. Where are we up to? Can we set a date for switching to svn? How's the paper looking?
Update on CHEBI xps. Where are we up to? Can we set a date for switching to svn? How's the paper looking?

Revision as of 09:59, 14 February 2012

MINUTES: BECKY


Discussion item I

Update on CHEBI xps. Where are we up to? Can we set a date for switching to svn? How's the paper looking?

Discussion item II

Regulation by template cont.

AN EXAMPLE OF 'REGULATION BY'

PMID 10591965: FLO8-dependent transcriptional regulation

FLO8 is a transcriptional regulator that up-regulates transcription of numerous genes, whose gene products are required for various yeast processes:

  • FLO8 -> transcription of FLO1 gene -> FLO1 encodes a lectin involved in flocculation
  • FLO8 -> transcription of STA1 gene -> STA1 encodes a glucoamylase responsible for starch degradation
  • FLO8 -> transcription of FLO11 gene -> FLO11 gene encodes a cell-surface protein required for filamentous growth
Example of an existing GO term made to represent this:
positive regulation of starch catabolic process by positive regulation of transcription from RNA polymerase II promoter ; GO:0035957

This GO term doesn't tell the whole story though. You can't tell from GO:35957 that FLO8 is a transcription factor. FLO8 lies at the bottom of a signal transduction pathway. Any gene product in the signaling pathway could be annotated to GO:0035957.

nutrient signal -> receptor --> MAPK cascade --> FLO8 (a TF) -->up-regulation of target genes

For an image of an example pathway, see: http://mcb.asm.org/content/19/7/4874/F10.large.jpg

  • In some cases you know that the annotated gene is a TF. In many cases, they just knock-out a gene and see that expression of STA1 is reduced and therefore starch degradation is impaired. Can we cover both scenarios?


Discussion item III

Can we have 'MF regulates MF'?

E.g.
MAPK activity
--[posreg]MAPKK activity