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
 
!  GO Developers
 
!  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 Susan Tweedie (FlyBase)
 
|  Dr Alex Diehl<br/> (MGI/UB Medical School; <br/> GO curator/GO editor)
 
|  Dr Rebecca Foulger (GO Editorial)<br/>Dr Midori Harris (GO Editorial; TBC)<br/>Dr Paola Roncaglia (GO Editorial from March 2011)
 
|  Chris Mungall (Berkeley)<br/> (Thursday only)
 
|  Dr Andrea Townsend-Nicholson (UCL)<br/>Dr Andrew Winter (University 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.
 
 
 
== Accommodation ==
 
 
 
The following participants have rooms reserved on site for the nights of Tuesday 15th and Wednesday 16th February:
 
*Dr Andrew Winter
 
*Dr Andrew Chatr-aryamontri
 
*Dr Andrea Townsend-Nicholson
 
*Dr Ruth Lovering
 
 
 
The following participants have rooms reserved on site for the nights of Wednesday 16th February:
 
*Dr Varsha Khodiyar
 
 
 
The following participants have rooms reserved on site for the nights of Monday 14th, Tuesday 15th, Wednesday 16th and Thursday 17th February.
 
*Dr Paola Roncaglia
 
 
 
All other participants are local or have arranged their own accommodation. Please let Rebecca know if this changes.
 
 
 
== Dinners ==
 
 
 
*For participants arriving on the Tuesday, and for anyone else who would like to join us, a meal will be arranged on Tuesday 15th February at the Hinxton Red Lion.
 
 
 
The Red Lion Menu's are available here: Please send Rebecca your choices by Friday 4th February.
 
 
 
[http://gocwiki.geneontology.org/images/8/8e/Bar_menu_Jan_2011_RedLionHinx.pdf Bar]
 
[http://gocwiki.geneontology.org/images/e/ea/A_la_carte_Jan_2011_RedLionHinx.pdf Alacarte]
 
[http://gocwiki.geneontology.org/images/7/7a/Puddings_jan_2011_RedLionHinx.pdf puddings]
 
 
 
*A workshop meal will be arranged for Wednesday 16th February at the John Barleycorn in Duxford. Menu is [http://gocwiki.geneontology.org/images/e/ee/JohnBarleyCorn_Menuamended.pdf here]
 
 
 
*Lunches on the Wednesday and Thursday will be at the on-site Murrays restaurant. Lunch vouchers will be provided for all participants.
 
 
 
*Tea and Coffee will be provided in the meeting rooms
 
 
 
== FUNDING ==
 
 
 
The GO signaling workshop is jointly funded by GO (75%) and UCL-BHF (25%).
 
 
 
The EBI Industry Programme, lead by Dominic Clark, is kindly funding the lunches and the workshop dinner on the Wednesday evening.
 
 
 
 
 
 
 
== Programme ==
 
 
 
Wednesday 16th February
 
 
 
*Morning Minutes: Varsha Khodiyar
 
*Afternoon Minutes: Susan Tweedie
 
 
 
{| 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'''
 
|[http://gocwiki.geneontology.org/images/7/70/Signalworkshopintro.pdf Introduction] to GO
 
|Rebecca
 
|-valign="top"
 
|'''9:50am'''
 
|Definition and Scope of signaling
 
|
 
|-valign="top"
 
|
 
|Definition of 'Signal Generation'
 
|
 
|-valign="top"
 
|
 
|Definition of 'Signal Transduction', including 'initiation' and 'termination'
 
|
 
|-valign="top"
 
|'''11am'''
 
|'''Coffee break'''
 
|
 
|-valign="top"
 
|'''11:20am'''
 
|Signaling pathways- how to define and group
 
|
 
|-valign="top"
 
|
 
|Non-1:1 receptor-ligand combinations
 
|
 
|-valign="top"
 
|'''12:30pm'''
 
|'''Lunch @ on-site campus restaurant'''
 
|
 
|-valign="top"
 
|'''1:45pm'''
 
|The function of being a receptor
 
|
 
|-valign="top"
 
|
 
|Nuclear hormone receptors
 
|
 
|-valign="top"
 
|
 
|Defining Intracellular 'cassettes'
 
|
 
|-valign="top"
 
|'''3:00 pm'''
 
|'''Coffee break'''
 
|
 
|-valign="top"
 
|
 
|Connecting Intracellular 'cassettes' with upstream receptors
 
|
 
|-valign="top"
 
|
 
|Receptor-mediated endocytosis and signaling
 
|
 
|-valign="top"
 
|
 
|Transport of the ligand to the receiving cell- endocrine/paracrine signaling
 
|
 
|-valign="top"
 
|
 
|Calcium-mediated signaling
 
|
 
|-valign="top"
 
|'''5:30pm'''
 
|'''Close'''
 
|
 
|}
 
 
 
 
 
Thursday 17th February
 
 
 
Morning Minutes: Rachael Huntley
 
Afternoon Minutes: Susan Tweedie
 
 
 
{| 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
 
|Sandra
 
|-valign="top"
 
|
 
|Oustanding/Unresolved issues from Wednesday
 
|Sandra and Ruth
 
|-valign="top"
 
|'''10am'''
 
|Chris will present work he's doing making automatic links between Reactome and GO signaling terms
 
|Chris Mungall
 
|-valign="top"
 
|'''10:30am'''
 
| Work through the insulin receptor signaling pathway to create a curation manual for annotators
 
|Sandra and Ruth
 
|-valign="top"
 
|
 
|Ligand-Receptor binding
 
|
 
|-valign="top"
 
|
 
|Proteins downstream of ligand-receptor binding: Signaling via IRS1. Signaling via SHC/MAPK.
 
|
 
|-valign="top"
 
|'''11am'''
 
|'''Coffee break'''
 
|
 
|-valign="top"
 
|
 
|Pathway regulators
 
|
 
|-valign="top"
 
|
 
|Proteins upstream of ligand-receptor binding: Insulin synthesis and secretion. Insulin receptor synthesis and processing.
 
|
 
|-valign="top"
 
|'''12:30pm'''
 
|'''Lunch @ on-site campus restaurant'''
 
|
 
|-valign="top"
 
|'''1:45pm'''
 
|Proteins involved in receptor-mediated endocytosis of ligand-receptor
 
|
 
|-valign="top"
 
|'''3:00 pm'''
 
|'''Close... Thank you all very much'''
 
|
 
|}
 
 
 
== 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 ==
 
 
 
 
 
A presentation on all the signaling topics is [http://gocwiki.geneontology.org/images/c/c0/Signalworkshop_problems.pdf here]
 
 
 
 
 
*<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="orange">Defining initiation of signal transduction:</font color>
 
***Currently used to annotate both ligands and receptors- is this correct?
 
***Which of its children do we want to keep?
 
 
 
*<font color="teal">Defining 'creation of a signal':</font color>
 
**Where does the process start... transcription/translation or later?
 
 
 
*<font color="grey">Receptor processing:</font color>
 
**Should receptor processing terms go under 'signaling' to be siblings with the 'creation of a signal' term?
 
**OR should receptor processing terms go under 'regulation of signaling'?
 
 
 
*<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="blue">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 15:49, 14 July 2014

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PLEASE SEE THE REVISED PAGE AT:

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