Difference between revisions of "2012 PAINT"

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DAY 1 PM
 
DAY 1 PM
  
* Walk though an example: CCS
+
* Walk though an example: PTHR10003 (CCS)
 
* The goal is to get everyone familiar with the PAINT tool.
 
* The goal is to get everyone familiar with the PAINT tool.
  
  
 
BREAK
 
BREAK
* First common example (TBD - easy)
+
* First common example: PTHR19443 (Hexokinase)
 
** MF annotation
 
** MF annotation
 
** MF discussion
 
** MF discussion
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* Simple examples
 
* Simple examples
**PTHR19443 (Hexokinase) - A classic example of protein families involved in metabolic pathways.
+
** - A classic example of protein families involved in metabolic pathways.
 
* Families with lots of duplications from the root, with new BP in recent species.
 
* 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.  
 
**PTHR11537 (Kv channela) - A typical example of families of ion channels, transporters and receptors with lots of gene duplications.  

Revision as of 13:49, 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 a more complicated example

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)


  • 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

  • Simple examples
    • - 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.
  • Transcription factors
    • PTHR11829 (Transcription factor)
  • Very complicated families
    • 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

Pascale