2012 PAINT

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

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.


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

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

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.

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 (bcl-2) - Too many GO terms. How to prioritize?
  • ??
    • PTHR13697 (Phosphofructokinase)
    • PTHR11361? Example of loss of function / stop propagation / add new function without loss


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)