Ontology meeting 2012-02-15: Difference between revisions

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(Created page with "===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...")
 
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===Discussion item II===
===Discussion item II===
Regulation by template cont.
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
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?

Revision as of 09:46, 14 February 2012

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

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?