2012 PAINT

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

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Preliminary agenda

DAY 1 9am-noon

• Introduction to evolution of gene families and function (Paul)
• PAINT: overview and general utilities (Huaiyu)

DAY 1 1pm-5pm

• 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

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DAY 2 9am

• 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.

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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

• Gene duplications
  • PTHR19957 (Syntaxin) - similar as above.
• Transcription factors
  • PTHR11829 (Transcription factor)
• Very complicated families
  • PTHR11256 (bcl-2) - Too many GO terms. How to prioritize?
• ??
  • PTHR13697 (Phosphofructokinase)
  • 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

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)