2012 PAINT: Difference between revisions

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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 16:56, 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)