Non 1:1 receptor:ligand binding: Difference between revisions

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[[Category:Signaling]]
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For the problems and proposed solutions to the issue of non 1:1 receptor:ligand binding, see slides 22-25 of the [http://wiki.geneontology.org/images/6/62/Signaling_LA_May2011.pdf overview] from the LA GOC meeting, May 2011.
It's well known that there is cross-talk amongst ligands and receptors, particularly within the growth factors. To represent this in GO, we will most likely require terms for:
 
* ligand-activated signaling pathways (E.g. VEGF-activated signaling pathway)
* receptor signaling pathways (E.g. PDGF receptor signaling pathway: MOST EXISTING TERMS ARE IN THIS FORMAT)
* Combination terms (E.g. VEGF-activated PDGF receptor signaling pathway)
 
For more detail, see slides 22-25 of the [http://wiki.geneontology.org/images/6/62/Signaling_LA_May2011.pdf overview] from the LA GOC meeting, May 2011.
 
The main issue is that in function the activity of the PDGFR is to bind PDGF and transmit a signal. To represent cross-talk. PDGFR signaling (in process) would refer to the gene product called PDGF, which can be activated by multiple ligands (including non-PDGFs). To make this less-confusing (as agreed in the May 2011 GOC meeting), I've changed the function terms for the growth factor receptors from 'platelet-derived growth factor receptor activity' to 'platelet-derived growth factor-ACTIVATED receptor activity'. With the addition of a HAS_PART link to 'PDGF binding', the activity is restricted to signaling from PDGF.
 
 
==Related SourceForge Items==
 
* Hormone and hormone receptor signaling pathways: https://sourceforge.net/tracker/?func=detail&aid=2974691&group_id=36855&atid=440764
* Norrin signaling: https://sourceforge.net/tracker/?func=detail&aid=3041964&group_id=36855&atid=440764
 
 
==Related Articles==
 
* VEGF can signal through platelet-derived growth factor receptors: PMID 17470632
* PDGF signaling in cells and mice. Figure 1 shows the preference of various PDGF members for PDGFRs: PMID 15207812
 
 
==Edits Done==
 
===End 2011===
 
Changed the function terms for the growth factor receptors '''FROM''' 'platelet-derived growth factor receptor activity' '''TO''' 'platelet-derived growth factor-ACTIVATED receptor activity'. With the addition of a HAS_PART link to 'PDGF binding', the activity is restricted to signaling from PDGF.
 
 
===February 2012===
 
Added terms to describe VEGF-PDGFR signaling (PMID 17470632; see above):
 
vascular endothelial growth factor signaling pathway ; GO:0038084
vascular endothelial growth factor binding ; GO:0038085
VEGF-activated platelet-derived growth factor receptor signaling pathway ; GO:0038086
VEGF-activated platelet-derived growth factor receptor-alpha signaling pathway ; GO:0038087
VEGF-activated platelet-derived growth factor receptor-beta signaling pathway ; GO:0038088

Latest revision as of 15:16, 30 June 2014

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Return to Signaling Main Page [[1]]


It's well known that there is cross-talk amongst ligands and receptors, particularly within the growth factors. To represent this in GO, we will most likely require terms for:

  • ligand-activated signaling pathways (E.g. VEGF-activated signaling pathway)
  • receptor signaling pathways (E.g. PDGF receptor signaling pathway: MOST EXISTING TERMS ARE IN THIS FORMAT)
  • Combination terms (E.g. VEGF-activated PDGF receptor signaling pathway)

For more detail, see slides 22-25 of the overview from the LA GOC meeting, May 2011.

The main issue is that in function the activity of the PDGFR is to bind PDGF and transmit a signal. To represent cross-talk. PDGFR signaling (in process) would refer to the gene product called PDGF, which can be activated by multiple ligands (including non-PDGFs). To make this less-confusing (as agreed in the May 2011 GOC meeting), I've changed the function terms for the growth factor receptors from 'platelet-derived growth factor receptor activity' to 'platelet-derived growth factor-ACTIVATED receptor activity'. With the addition of a HAS_PART link to 'PDGF binding', the activity is restricted to signaling from PDGF.


Related SourceForge Items


Related Articles

  • VEGF can signal through platelet-derived growth factor receptors: PMID 17470632
  • PDGF signaling in cells and mice. Figure 1 shows the preference of various PDGF members for PDGFRs: PMID 15207812


Edits Done

End 2011

Changed the function terms for the growth factor receptors FROM 'platelet-derived growth factor receptor activity' TO 'platelet-derived growth factor-ACTIVATED receptor activity'. With the addition of a HAS_PART link to 'PDGF binding', the activity is restricted to signaling from PDGF.


February 2012

Added terms to describe VEGF-PDGFR signaling (PMID 17470632; see above): 

vascular endothelial growth factor signaling pathway ; GO:0038084
vascular endothelial growth factor binding ; GO:0038085 
VEGF-activated platelet-derived growth factor receptor signaling pathway ; GO:0038086
VEGF-activated platelet-derived growth factor receptor-alpha signaling pathway ; GO:0038087
VEGF-activated platelet-derived growth factor receptor-beta signaling pathway ; GO:0038088
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