Difference between revisions of "Signaling Workshop February 2010"

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**signal transmission
**signal transmission
**signaling pathway
**signaling pathway
*<font color="orange">Defining and placing:</font color>
**iniation of signal transduction and its children
***Currently used to annotate both ligands and receptors- is this correct?
***Which of its children do we want to keep?
*<font color="green">Connecting the networks</font color>
*<font color="green">Connecting the networks</font color>

Revision as of 03:16, 14 December 2010

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Return to Signaling Main Page [[1]]

Please suggest agenda items, relevant papers and other information relating to signaling GO terms that you would like discussed at this workshop.


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 Susan Tweedie (FlyBase)
Dr Alex Diehl
(MGI/UB Medical School; GO curator/GO editor)
Dr Rebecca Foulger (GO Editorial)
Dr Midori Harris (GO Editorial; TBC)
Dr Paola Roncaglia (GO Editorial from Feb 2011)
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.


The following participants have rooms reserved on site for the nights of Tuesday 14th and Wednesday 15th February:

  • Dr Andrew Winter
  • Dr Andrew Chatr-aryamontri
  • Dr Andrea Townsend-Nicholson

The following participants have rooms reserved on site for the nights of Wednesday 15th February:

  • Dr Ruth Lovering
  • Dr Varsha Khodiyar

All other participants are local or have arranged their own accommodation. Please let Rebecca know if this changes.


  • For participants arriving on the Tuesday, and for anyone else who would like to join us, a meal will be arranged on Tuesday 14th February near campus (probably at the Hinxton Red Lion).
  • A workshop meal will be arranged for Wednesday 15th February near campus (probably at the John Barleycorn in Duxford).
  • 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


Wednesday 16th February

9:15am Tea and Coffee
9:30am Welcome and introduction Rebecca
9:35am Introduction to GO Rebecca
11am Coffee break
12:30pm Lunch @ on-site campus restaurant
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 Work through INSR signaling pathway to create curation manual for annotators
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)


  • How the signaling node should be split
    • cellular vs tissue vs organismal?
    • pathway vs process?
  • Defining and placing:
    • signal transduction
    • signal transmission
    • signaling pathway
  • Defining and placing:
    • iniation of signal transduction and its children
      • Currently used to annotate both ligands and receptors- is this correct?
      • Which of its children do we want to keep?
  • 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?
    • 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?
    • 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



Definition Adjustments:

Obsoleted Terms:

Moved Terms:

New Terms: