Difference between revisions of "Signaling Workshop February 2010"

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*Morning Minutes: Varsha Khodiyar
*Morning Minutes: Varsha Khodiyar
*Afternoon Minutes: Susan Tweedie
*Afternoon Minutes: Susan Tweedie
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Thursday 17th February
Thursday 17th February
Morning Minutes: Rachael Huntley
*Morning Minutes: Rachael Huntley
Afternoon Minutes: Susan Tweedie
*Afternoon Minutes: Susan Tweedie
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Revision as of 08:44, 27 January 2011

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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 GO Developers 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 March 2011)
Chris Mungall (Berkeley)
(Thursday only)
Dr Andrea Townsend-Nicholson (UCL)
Dr Andrew Winter (University 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 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.


  • 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.

Bar Alacarte puddings

  • A workshop meal will be arranged for Wednesday 16th February at the John Barleycorn in Duxford. Menu is 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


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.


Wednesday 16th February

  • Morning Minutes: Varsha Khodiyar
  • Afternoon Minutes: Susan Tweedie

9:15am Tea and Coffee
9:30am Welcome and introduction Rebecca
9:35am Introduction to GO Rebecca
9:50am Definition and Scope of signaling
Definition of 'Signal Generation'
Definition of 'Signal Transduction', including 'initiation' and 'termination'
11am Coffee break
11:20am Signaling pathways- how to define and group
Non-1:1 receptor-ligand combinations
12:30pm Lunch @ on-site campus restaurant
1:45pm The function of being a receptor
Nuclear hormone receptors
Defining Intracellular 'cassettes'
3:00 pm Coffee break
Connecting Intracellular 'cassettes' with upstream receptors
Receptor-mediated endocytosis and signaling
Transport of the ligand to the receiving cell- endocrine/paracrine signaling
Calcium-mediated signaling
5:30pm Close

Thursday 17th February

  • Morning Minutes: Rachael Huntley
  • Afternoon Minutes: Susan Tweedie

9:15am Tea and Coffee
9:30am Recap of decisions made on Day 1 Sandra
Oustanding/Unresolved issues from Wednesday Sandra and Ruth
10am Chris will present work he's doing making automatic links between Reactome and GO signaling terms Chris Mungall
10:30am Work through the insulin receptor signaling pathway to create a curation manual for annotators Sandra and Ruth
Ligand-Receptor binding
Proteins downstream of ligand-receptor binding: Signaling via IRS1. Signaling via SHC/MAPK.
11am Coffee break
Pathway regulators
Proteins upstream of ligand-receptor binding: Insulin synthesis and secretion. Insulin receptor synthesis and processing.
12:30pm Lunch @ on-site campus restaurant
1:45pm Proteins involved in receptor-mediated endocytosis of ligand-receptor
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)


A presentation on all the signaling topics is here

  • 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 initiation of signal transduction:
      • Currently used to annotate both ligands and receptors- is this correct?
      • Which of its children do we want to keep?
  • Defining 'creation of a signal':
    • Where does the process start... transcription/translation or later?
  • Receptor processing:
    • 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'?
  • 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: