Signaling Workshop February 2010
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Please suggest agenda items, relevant papers and other information relating to signaling GO terms that you would like discussed at this workshop.
Participants
GO Annotators | Remote Participants | GO Editors | Signaling Experts |
---|---|---|---|
Dr Ruth Lovering (BHF-UCL) Dr Varsha Khodiyar (BHF-UCL) Dr Sandra Orchard (Intact) Dr Peter D'Eustachio (Reactome) Dr Rachael Huntley(GOA) Dr Val Wood (PombeBase) Dr Alex Diehl (MGI) (TBC) |
Dr Alex Diehl (MGI/UB Medical School; GO curator and editor and Cell ontology editor) |
Dr Rebecca Foulger (GO Editorial) Dr Midori Harris (GO Editorial) |
Dr Andrea Townsend-Nicholson (UCL) Dr Andrew Winter (Univeristy Edinburgh) Dr Andrew Chatr-aryamontri (University Edinburgh) |
Where and When
Date: Wednesday 16th February and Thursday 17th February, 2011.
Where: EMBL-EBI.
Wednesday: A2-33 Thursday: Courtyard room
- Travel instructions to the EBI, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD [2]
- Please let EBI reception know you have arrived, and Rebecca will come and meet you.
Programme
Wednesday 16th February
9:15am | Tea and Coffee | |
9:30am | Welcome and introduction | Rebecca |
9:35am | Introduction to GO | Rebecca |
9:50am | ||
11am | Coffee break | |
11:45am | ||
12:30pm | Lunch @ on-site campus restaurant | |
2pm | ||
3:00 pm | Coffee break | |
5pm | Close |
Thursday 17th February
9:15am | Tea and Coffee | |
9:30am | Recap of decisions made on Day 1. | Rebecca |
10am | ||
11am | Coffee break | |
12:30pm | Lunch @ on-site campus restaurant | |
3:00 pm | Close |
Relevant papers and other resources
Biochemistry of Signal Tranduction and Regulation. Gerhard Krauss. ISBN:3-527-29241-1
Cell Signaliing. John T. Hancock. ISBN:0199264678
The Biochemistry of Cell Signalling. Ernst J. M. Helmreich. ISBN: 0198508204
Signal Transduction. Gompert et al. ISBN: 9787030182173. (recommended by Andrea: provides a history on signal transduction)
Topics
- How the signaling node should be split
- cellular vs tissue vs organismal?
- pathway vs process?
- Defining and placing:
- signal transduction
- signal transmission
- signaling pathway
- Connecting the networks
- How to connect the cell surface receptors with the intracellular 'modules' they signal through
- Dealing with ligand-receptor signaling that is not 1:1
- What is a signal transducer?
- receptors?
- ligands?
- downstream kinases?
- RECEPTORS
- Should ligand-gated ion channels be given receptor parents?
- Should receptors be divided into 'transport receptors' that deliver nutrients into the cell, and 'signaling receptors' that transduce a signal.
- Should the RECEPTOR terms be kept in FUNCTION, or PROCESS terms created to replace them?
- signal reception (synonym: receptor)
- primary signal transduction (synonym: receptor)
- receptor-mediated endocytosis
- How should receptor-mediated endocytosis be linked to signaling?
- Is the first step in RME (receptor binding to nutrient/ligand) signal transduction?
- Where do RME receptors (eg LDLR, transferrin receptor) fit in?
- CELL CYCLE CHECKPOINTS (Val)
- How do the checkpoints fit with the signal transduction terms.
- Val has been in contact with Paul Russell about checkpoints: He said: the term DNA damage checkpoint would represent the gene products involved in signalling only.
- Connecting the signaling terms and response terms
SourceForge Signaling Items
receptors and HAS_PART: http://sourceforge.net/tracker/?func=detail&aid=3103037&group_id=36855&atid=440764
receptor signaling proteins: http://sourceforge.net/tracker/?func=detail&aid=3101487&group_id=36855&atid=440764
purigenic receptors: http://sourceforge.net/tracker/?func=detail&aid=3088079&group_id=36855&atid=440764
MAPKKK cascade: http://sourceforge.net/tracker/?func=detail&aid=3085150&group_id=36855&atid=440764
Calcium-mediated signaling; http://sourceforge.net/tracker/?func=detail&aid=3077377&group_id=36855&atid=440764
morphogen: http://sourceforge.net/tracker/?func=detail&aid=3026415&group_id=36855&atid=440764
norrin signaling (example of non 1:1 receptor:ligand signaling) : http://sourceforge.net/tracker/?func=detail&aid=3041964&group_id=36855&atid=440764
hormone and hormone receptor signaling: http://sourceforge.net/tracker/?func=detail&aid=2974691&group_id=36855&atid=440764
Connecting up receptors and intracellular modules:
wnt signaling via hippo cascade: http://sourceforge.net/tracker/?func=detail&aid=3032564&group_id=36855&atid=440764
wnt signaling via JNK cascade: http://sourceforge.net/tracker/?func=detail&aid=3023417&group_id=36855&atid=440764
PI3K/AKT signaling: http://sourceforge.net/tracker/?func=detail&aid=3008502&group_id=36855&atid=440764
Minutes
Notes
Definition Adjustments:
Obsoleted Terms:
Moved Terms:
New Terms: