March 25th 2010: Difference between revisions

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I don't know if we want a term 'cellular signaling ; GO:NEW', or if this would complicate things?
I don't know if we want a term 'cellular signaling ; GO:NEW', or if this would complicate things?


Also, should cell-cell signaling really be under signal transmission ; GO:0023060 ?


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intracellular signaling pathway ; GO:0023034
intracellular signaling pathway ; GO:0023034
intracellular receptor-mediated signaling pathway ; GO:0030522
intracellular receptor-mediated signaling pathway ; GO:0030522
signal transmission via intracellular cascade ; GO:0023013 (not sure where this fits in)


A few points here:
A few points here:
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signal transduction ; GO:0007165
signal transduction ; GO:0007165


<nowiki>--</nowiki>%intracellular signal transduction ; GO:NEW
<nowiki>--</nowiki>%intracellular signal transduction ; GO:NEW (is this the same as GO:0023013 ???)


<nowiki>----</nowiki>%intracellular protein kinase cascade ; GO:0007243 (RENAMED FROM protein kinase cascade)
<nowiki>----</nowiki>%intracellular protein kinase cascade ; GO:0007243 (RENAMED FROM protein kinase cascade)


<nowiki>----</nowiki>%second-messenger-mediated signaling ; GO:0019932
<nowiki>----</nowiki>%second-messenger-mediated signaling ; GO:0019932

Revision as of 12:24, 24 March 2010

Signaling Conference Call 2


Agenda

1. Relook at what processes are included in signaling ; GO:0023052 Current def: The entirety of a process whereby information is transmitted. This process begins with the initiation of the signal and ends when a response has been triggered. [this ties in with the next items]


2. Look at cell communication vs signaling. GO relationships are currently:

GO:0008150 biological_process

--GO:0023052 signaling

----%GO:0007154 cell communication

------%GO:0007267 cell-cell signaling


--%GO:0009987 cellular process

-----%GO:0007154 cell communication

The definition of GO:0007154 cell communication is broader than just signaling: Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.

A suggested rearrangement:

GO:0008150 biological_process

--GO:0023052 biological signaling (NAME CHANGE!!)

----%GO:0007267 cell-cell signaling

--GO:0009987 cellular process

----%GO:0007154 cell communication

------%GO:0007267 cell-cell signaling

I don't know if we want a term 'cellular signaling ; GO:NEW', or if this would complicate things?


Also, should cell-cell signaling really be under signal transmission ; GO:0023060 ?


3. Redefine GO:0023032 behavioral signaling

Current definition: The entirety of the behavioral process whereby information is sent between living organisms.

Suggested change:

GO:0051704 multi-organism process

--%GO:0023032 multi-organismal signaling

The entirety of a process whereby information is transmitted between organisms to have an effect on another organism of the same or different species.



4. Better define signaling pathway ;GO:0023033 Q: where does a pathway begin? ----is signal generation included?

----is signal release included?

----is receptor processing prior to ligand-binding included?

----is ligand processing prior to receptor-binding included?

At the moment the definitions of the individual pathways start with receptor-ligand binding: Notch signaling pathway ; GO:0007219 The series of molecular signals initiated by binding of an extracellular ligand to a Notch receptor on the surface of the target cell.

However, I would include upstream events (processing of the receptor (notch) prior to ligand binding) as being part of the pathway. We could change the definition to: The series of molecular signals resulting in and/or initiated by binding of an extracellular ligand to a Notch receptor on the surface of the target cell.

One problem is that signaling pathway is used interchangably with signal transduction in the literature. However if we restrict signaling pathways to events that occur only within one cell, then we create problems for things like auxin mediated signaling pathway ; GO:0009734 ----<auxin efflux ; GO:0010315

and smoothened signaling pathway ; GO:0007224 ----<patched ligand maturation ; GO:0007225



5. intracellular signaling

intracellular signaling cascade ; GO:0007242 intracellular signaling pathway ; GO:0023034 intracellular receptor-mediated signaling pathway ; GO:0030522 signal transmission via intracellular cascade ; GO:0023013 (not sure where this fits in)

A few points here:

I'd like to move GO:0030522 out from being a child of GO:0007242. The signal still has to be released by the signaling cell and enter the target cell so the whole pathway is not intracellular.

Val pointed out that people have been using GO:0007242 more generally than signal transduction, so we can merge it with GO:0023034. I would like to see GO:0023034 used ONLY for pathways that are entirely intracellular. At the moment, this would restrict it to: chloroplast-nucleus signaling pathway ; GO:0010019 mitochondrial signaling pathway ; GO:0031930

Suggested graph:

signaling ; GO:0023052 --%signaling pathway ; GO:0023033

----%cell surface receptor linked signaling pathway ; GO:0007166

----%intracellular receptor-mediated signaling pathway ; GO:0030522

----%intracellular signaling pathway ; GO:0023034

------%chloroplast-nucleus signaling pathway ; GO:0010019

------%mitochondrial signaling pathway ; GO:0031930

signal transduction ; GO:0007165

--%intracellular signal transduction ; GO:NEW (is this the same as GO:0023013 ???)

----%intracellular protein kinase cascade ; GO:0007243 (RENAMED FROM protein kinase cascade)

----%second-messenger-mediated signaling ; GO:0019932