Signaling Workshop February 2010: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
No edit summary
 
(26 intermediate revisions by one other user not shown)
Line 1: Line 1:
[[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.


----
PLEASE SEE THE REVISED PAGE AT:


 
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 Susan Tweedie (FlyBase)
|  Dr Alex Diehl<br/> (MGI/UB Medical School; GO curator/GO editor)
|  Dr Rebecca Foulger (GO Editorial)<br/>Dr Midori Harris (GO Editorial; TBC)<br/>Dr Paola Roncaglia (GO Editorial from Feb 2011)
|  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 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
 
The following participants have rooms reserved on site for the nights of Tuesday 14th, Wednesday 15th and Thursday 16th 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 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
 
 
 
== 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'''
|
|
|-valign="top"
|
|
|
|-valign="top"
|'''11am'''
|Coffee break
|
|-valign="top"
|'''11:45am'''
|
|
|-valign="top"
|'''12:30pm'''
|Lunch @ on-site campus restaurant
|
|-valign="top"
|'''2pm'''
|
|
|-valign="top"
|'''3:00 pm'''
|Coffee break
|
|-valign="top"
|
|
|
|-valign="top"
|'''5pm'''
|Close
|
|}
 
 
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'''
| Work through INSR signaling pathway to create curation manual for annotators
|
|-valign="top"
|
|
|
|-valign="top"
|
|
|
|-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="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 18:49, 14 July 2014

Return to GOC Main Page

Return to Signaling Main Page [[1]]


PLEASE SEE THE REVISED PAGE AT:

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