View source for 2012 PAINT

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

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Preliminary agenda

DAY 1 AM
* Introduction to evolution (Paul)
* PAINT: overview and general utilities (Huaiyu)


DAY 1 PM

* Walk though an example: CCS
* The goal is to get everyone familiar with the PAINT tool.


BREAK
* First common example (TBD - easy)
** MF annotation
** MF discussion


** CC annotation 
** CC discussion

** BP annotation 
** BP discussion



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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.
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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.


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List of possible examples for the workshop

* Simple examples
**PTHR19443 (Hexokinase) - 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

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Pascale

**PTHR10454 Caspase family
***PMID: 23070001
***PMID: 22949111
***PMID: 22606010
***http://en.wikipedia.org/wiki/Caspase
**PTHR19384 Nitric oxide synthase
***Excessive downstream processes