October 4th 2010

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AGENDA

1. signal transduction ; GO:0007165 & signaling pathway ; GO:0023033

signal transduction ; GO:0007165
The process whereby an activated receptor conveys information down the signaling pathway, resulting in a change in the function or  state of a cell.

signaling pathway ; GO:0023033
New proposed definition:
The series of molecular events whereby a signal is received, transmitted and interpreted. A signaling pathway begins with reception   of the signal, for example binding of a ligand to a receptor or activation of a receptor via a conformational change, and ends when a response has been triggered.

i/ Is the revised definition for 'signaling pathway ; GO:0023033' ok? Is the ligand part of the signaling pathway?

ii/ Look at the definition of signal transduction. When are we saying that signal transduction starts? Does it include the ligand? Does it include signal reception (ie initiation of signal transduction)? Current def: The process whereby an activated receptor conveys information down the signaling pathway, resulting in a change in the function or state of a cell.

iii/ Should there be a link between the high level terms 'signal tranduction' and 'signaling pathway'? Lots of people use 'pathway' and 'transduction' interchangably. Note: We've defined the pathway as including the ligand.

iv/ Look at current children of signal transduction. Do they belong there?

v/ In the original revisions, how were people defining signal transduction: the whole pathway or any one of the individual steps in the signaling pathway?

vi/ Should we add a comment to 'signaling pathway ; GO:0023033' E.g. This term is intended to group the collection of signal molecules that work together to convert a signal into a cellular response.



2. receptor ligand activity


Choose from two options:

ii/ Add 'receptor ligand activity' as a broad synonym to the existing terms:
receptor agonist activity ; GO:0048018
and?
receptor antagonist activity ; GO:0048019

OR

ii/ Create a new 'receptor ligand' term as a parent:
receptor binding
--%receptor ligand activity ; GO:NEW
----%receptor antagonist activity ; GO:0048019
----%receptor agonist activity ; GO:0048018

receptor ligand activity ; GO:NEW
Binding to a receptor to alter the proportion of receptors in an active form.

3. receptor-mediated endocytosis

See [1]

  • How do we deal with receptors that aren't involved in signaling? E.g. those involved in receptor-mediated endocytosis.
  • Need to revise the definition of signal transducer activity ; GO:0004871

Mediates the transfer of a signal from the outside to the inside of a cell by means other than the introduction of the signal molecule itself into the cell.

Suggested revisions:

i/ Update definition of 'signal transducer activity ; GO:0004871' to:

Converts a chemical or mechanical stimulus from one form to another to initiate a change in cell state or activity. (maybe leave the revision until we look more closely at the function terms)

ii/ Move 'receptor activity' out from under signal transduction and create child terms:

molecular function
--%receptor activity
----%signaling receptor activity ; GO:NEW
----%endocytosis-stimulating receptor activity ; GO:NEW

signal transducer activity
--%signaling receptor activity ; GO:NEW
  • (we'd need to look at the current children of 'receptor activity' to see if they can be partitioned)

iii/ ADD a relationship in the process node:

negative regulation of signal transduction ; GO:0009968
--%receptor internalization ; GO:0031623

iv/ Which receptor terms should go under 'signaling process'.

  • receptor clustering ; GO:0043113
  • signal complex assembly ; GO:0007172
  • receptor metabolic process ; GO:0043112
  • receptor internalization ; GO:0031623



4. consequence of signal transmission ; GO:0023050

Discuss proposal to obsolete GO:0023050



5. Intracellular signaling

  • Discuss proposal to obsolete 'intracellular signaling pathway ; GO:0023034'
  • Would generate:
signaling pathway ; GO:0023033
--<intracellular signal transduction ; GO:0035556 (aka intracellular signaling cascade)