Difference between revisions of "Signaling Workshop February 2010"

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[[Category:Signaling]]
 
Return to [[Main_Page|GOC Main Page]]
 
Return to [[Main_Page|GOC Main Page]]
  
 
Return to Signaling Main Page [[http://wiki.geneontology.org/index.php/Signaling]]
 
Return to Signaling Main Page [[http://wiki.geneontology.org/index.php/Signaling]]
  
Please suggest agenda items, relevant papers and other information relating to signaling GO terms that you would like discussed at this workshop.
 
  
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PLEASE SEE THE REVISED PAGE AT:
  
 
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http://gocwiki.geneontology.org/index.php/Signaling_Workshop_February_2011
== Participants ==
 
 
 
{| class="wikitable" border="1"
 
|-
 
!  GO Annotators
 
!  Remote Participants
 
!  GO Editors
 
!  Signaling Experts
 
|-
 
|  Dr Ruth Lovering (BHF-UCL)<br/>Dr Varsha Khodiyar (BHF-UCL)<br/>Dr Sandra Orchard (Intact)<br/>Dr Peter D'Eustachio (Reactome) <br/>Dr Rachael Huntley(GOA)  <br/>Dr Val Wood (PombeBase)<br/>Dr Alex Diehl (MGI) (TBC)
 
|  Dr Alex Diehl<br/> (MGI/UB Medical School; GO curator and editor)
 
|  Dr Rebecca Foulger (GO Editorial)<br/>Dr Midori Harris (GO Editorial)
 
|  Dr Andrea Townsend-Nicholson (UCL)<br/>Dr Andrew Winter (Univeristy Edinburgh)<br/>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 [http://www.ebi.ac.uk/Information/Travel/travel.html]
 
 
 
* Please let EBI reception know you have arrived, and Rebecca will come and meet you.
 
 
 
 
 
 
 
== Programme ==
 
Wednesday 16th February
 
 
 
{| border="1" cellpadding="2" width=1000px
 
|-valign="top"
 
|width="5%"|'''9:15am'''
 
|width="90%"|Tea and Coffee
 
|width="5%"|
 
|-valign="top"
 
|'''9:30am'''
 
| Welcome and introduction
 
|Rebecca
 
|-valign="top"
 
|'''9:35am'''
 
|Introduction to GO
 
|Rebecca
 
|-valign="top"
 
|'''9:50am'''
 
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|-valign="top"
 
|'''11am'''
 
|Coffee break
 
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|'''11:45am'''
 
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|-valign="top"
 
|'''12:30pm'''
 
|Lunch @ on-site campus restaurant
 
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|'''2pm'''
 
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|-valign="top"
 
|'''3:00 pm'''
 
|Coffee break
 
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|-valign="top"
 
|'''5pm'''
 
|Close
 
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|}
 
 
 
 
 
Thursday 17th February
 
 
 
{| border="1" cellpadding="2" width=1000px
 
|-valign="top"
 
|width="5%"|'''9:15am'''
 
|width="90%"|Tea and Coffee
 
|width="5%"|
 
|-valign="top"
 
|'''9:30am'''
 
| Recap of decisions made on Day 1.
 
|Rebecca
 
|-valign="top"
 
|'''10am'''
 
|
 
|
 
|-valign="top"
 
|
 
|
 
|
 
|-valign="top"
 
|
 
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|
 
|-valign="top"
 
|'''11am'''
 
|Coffee break
 
|
 
|-valign="top"
 
|
 
|
 
|
 
|-valign="top"
 
|'''12:30pm'''
 
|Lunch @ on-site campus restaurant
 
|
 
|-valign="top"
 
|
 
|
 
|
 
|-valign="top"
 
|'''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 ==
 
 
 
*<font color="blue">How the signaling node should be split</font color>
 
**cellular vs tissue vs organismal?
 
**pathway vs process?
 
 
 
*<font color="purple">Defining and placing:</font color>
 
**signal transduction
 
**signal transmission
 
**signaling pathway
 
 
 
*<font color="green">Connecting the networks</font color>
 
**How to connect the cell surface receptors with the intracellular 'modules' they signal through
 
 
 
*<font color="red">Dealing with ligand-receptor signaling that is not 1:1</font color>
 
 
 
*<font color="magenta">What is a signal transducer?</font color>
 
**receptors?
 
**ligands?
 
**downstream kinases?
 
 
 
*<font color="burgundy">RECEPTORS</font color>
 
**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)
 
 
 
*<font color="orange">receptor-mediated endocytosis</font color>
 
**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?
 
 
 
*<font color="navy">CELL CYCLE CHECKPOINTS (Val)</font color>
 
**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.
 
 
 
*<font color="violet">Connecting the signaling terms and response terms</font color>
 
 
 
== 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:
 

Latest revision as of 14:49, 14 July 2014

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PLEASE SEE THE REVISED PAGE AT:

http://gocwiki.geneontology.org/index.php/Signaling_Workshop_February_2011