2012 PAINT: Difference between revisions
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**PTHR10454 Caspase family | **PTHR10454 Caspase family | ||
PMID: 23070001 | |||
PMID: 22949111 | |||
PMID: 22606010 | |||
http://en.wikipedia.org/wiki/Caspase |
Revision as of 18:17, 4 December 2012
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
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)
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
- 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
Pascale
- PTHR10454 Caspase family
PMID: 23070001 PMID: 22949111 PMID: 22606010 http://en.wikipedia.org/wiki/Caspase