2010 GO camp Use of Regulation issues

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Revision as of 08:15, 14 April 2010 by Edimmer (talk | contribs) (1. Background)

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1. Background

David Hill's slides

2. Review of current GO annotation practices

Question 1: How do groups decide on when to annotate to 'regulates process x' or 'process x'? For instance does SLIT regulate axon guidance or involved in the process of axon guidance? Val - this depends on the defined start/end of a process and somethings can be annotated to BOTH the regulates term and also directly to the process term. Some groups decide that if removing the activity of a gene product produces an all/nothing event - then they define it as being part of the process. When should annotations be inherited up the regulates relationship?

Question 2: Annotations could be checked more efficiently if GO term definitions could include the beginning and end of a process.

Question 3 (from Ruth): Should we also consider how the 'activity' of a protein is defined when making these regulation/process decisions. The definition for transcription factor activity is: The function of binding to a specific DNA sequence in order to modulate transcription.... This suggests that a transcription factor is involved in the process of regulating transcription rather than involved in the process of transcription itself. However, some of us in the UK feel that many transcription factors are involved in the transcription process itself definition: The synthesis of either RNA on a template of DNA or DNA on a template of RNA. Does the definition for transcription factor activity need modification to enable this annotation, or are only the polymerases involved in the synthesis?)

Question 3: Regulation of processes, especially with IMP;

  • example 1: [1]

3. Proposed annotation policy

4. Examples (papers) and discussion of GO annotation issues

Example 1 (from Rachael): PMID:19424712 - Ang1 is the ligand for TIE2, so it activates TIE2 which is then internalized and degraded. (Fig. 5a) HUVECs were incubated with Ang1 and the amount of Tie2 remaining at cell surface was decreased, therefore it has been internalized - question is whether Ang1 should be annotated to the process 'receptor internalization' or the regulation of? Or is GO:0007171 'activation of transmembrane receptor protein tyrosine kinase activity' enough?

5. Suggestions for Quality Control procedures


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