Difference between revisions of "2012 PAINT"

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DAY 2 AM
 
DAY 2 AM
  
* Walk through a more complicated example
+
* Walk through more complicated examples
 +
** PTHR11537 (Kv channel)
 +
** PTHR11254 (Ubiquitin protein ligase)
 +
** PTHR19384 Nitric oxide synthase
 +
***Excessive downstream processes
  
We need to define types of examples with specific issues: 
 
** Families where a member has lost a function
 
WE NEED TO START A TABLE with types
 
  
 
Part of BP discussion:
 
* Annotations to be cautious about (Pascale)
 
** Regulation of tyrosine hydroxylase activity
 
** Activation of transcription factors, including production of downstream proteins (interleukins)
 
  
  
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List of possible examples for the workshop
 
List of possible examples for the workshop
  
* Simple examples
+
* Gene duplications
** - A classic example of protein families involved in metabolic pathways.
 
* Families with lots of duplications from the root, with new BP in recent species.
 
**PTHR11537 (Kv channela) - A typical example of families of ion channels, transporters and receptors with lots of gene duplications.
 
 
**PTHR19957 (Syntaxin) - similar as above.
 
**PTHR19957 (Syntaxin) - similar as above.
 
*Transcription factors
 
*Transcription factors
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**PTHR11256 (blc-2) - Too many GO terms. How to prioritize?
 
**PTHR11256 (blc-2) - Too many GO terms. How to prioritize?
 
*??
 
*??
**PTHR11354 (Ubiquitin protein ligase)
+
**
 
**PTHR11361? Example of loss of function / stop propagation / add new function without loss
 
**PTHR11361? Example of loss of function / stop propagation / add new function without loss
  
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***PMID: 22606010
 
***PMID: 22606010
 
***http://en.wikipedia.org/wiki/Caspase
 
***http://en.wikipedia.org/wiki/Caspase
**PTHR19384 Nitric oxide synthase
+
Part of BP discussion:
***Excessive downstream processes
+
* Annotations to be cautious about (Pascale)
 +
** Regulation of tyrosine hydroxylase activity
 +
** Activation of transcription factors, including production of downstream proteins (interleukins)

Revision as of 13:56, 7 December 2012

PAINT User Guide: http://wiki.geneontology.org/index.php/PAINT_User_Guide


Preliminary agenda

DAY 1 AM

  • Introduction to evolution (Paul)
  • PAINT: overview and general utilities (Huaiyu)


DAY 1 PM

  • Walk though an example: PTHR10003 (CCS)
  • The goal is to get everyone familiar with the PAINT tool.


BREAK

  • First common example: PTHR19443 (Hexokinase)
    • MF annotation
    • MF discussion


    • CC annotation
    • CC discussion
    • BP annotation
    • BP discussion



DAY 2 AM

  • Walk through more complicated examples
    • PTHR11537 (Kv channel)
    • PTHR11254 (Ubiquitin protein ligase)
    • PTHR19384 Nitric oxide synthase
      • Excessive downstream processes



  • Dinner at Huaiyu's house in Palo Alto. Please plan accordingly.

DAY 3 & DAY 4

  • Everyone works on example trees.
  • One family each half day, 4 examples total
  • Leave an hour at the end of each half day for wrap-up discussion. One participant should present the annotation and lead the discussion.



List of possible examples for the workshop

  • Gene duplications
    • PTHR19957 (Syntaxin) - similar as above.
  • Transcription factors
    • PTHR11829 (Transcription factor)
  • Very complicated families
    • PTHR11256 (blc-2) - Too many GO terms. How to prioritize?
  • ??
    • PTHR11361? Example of loss of function / stop propagation / add new function without loss

Pascale

Part of BP discussion:

  • Annotations to be cautious about (Pascale)
    • Regulation of tyrosine hydroxylase activity
    • Activation of transcription factors, including production of downstream proteins (interleukins)