Signaling ontology structure documentation

From GO Wiki
Jump to navigation Jump to search

Top categories

[i]chemical substance-mediated signaling 
---[i]hydrophobic molecule-mediated signaling 
---[i]hydrophilic molecule-mediated signaling 
---[i]intracellular signaling
------[i]large intracellular mloecule-mediated signaling
---[i]intercellular signaling
[i]regulation of biological process by signaling 
---[i]regulation of gene expression by signaling
[i]signaling systems grouped by location of the signal molecule
---[i]cell surface receptor protein-mediated signaling
[i]long distance signaling
[i]short distance signaling
[i]molecular switch-like signaling
---[i]phosphoylation/dephosphorylation-mediated signaling
---[i]GTP-binding protein-mediated signaling
[i]regulation of signaling
---[i]process mediating persistance of signaling effect after signal has gone
---[i]process mediating response to signal molecule gradient
---[i]process of adjustment of sensitivity to signal
---[i]process of linking signals to alter response
------[i]scaffold protein-mediated regulation of signaling

Sub-groups

[i]hydrophobic molecule-mediated signaling 
---[i]nitrous oxide-mediated signaling
---[i]carbon monoxide-mediated signaling
[i]hydrophilic molecule-mediated signaling 
[i]signaling to control gene expression
---[i]primary response
---[i]secondary response

//distance is going to be problematic but this is how the book defines them. Also tricky between plants and animals.

[i]long distance signaling
---[i]long distance hormone-mediated signaling
---[i]long distance nervous system-mediated signaling
[i]short distance signaling
---[i]local mediators 
[i]endocrine signaling (signal to self)
[i]paracrine signaling (signal to someone else) 

We could deal with this using the standard expressions of size in GO.
e.g.
systemic signaling
cell-cell signaling
signaling within a tissue
organismal signaling
signaling within an organ



//large and small moleculaes are also going to be difficult.

[i]large intracellular molecule-mediated signaling
---[i]relay protein-mediated signaling
---[i]messenger protein-mediated signaling
---[i]adaptor protein-mediated signaling
---[i]amplifier protein-mediated signaling
---[i]transducer protein-mediated signaling
---[i]bifurcation protein-mediated signaling
---[i]integrator protein-mediated signaling
---[i]latent gene regulatory protein-mediated signaling

Small signals might be gtp, NO etc. We may not be able to classify them as small and large.

Perhaps instead use:

[i]signaling by diffusable molecular signal
[i]signaling by non-diffusable molecular signal

//These are a bit of a mouthful.

[i]cell surface receptor protein-mediated signaling
---[i]ion-channel linked cell surface receptor protein-mediated signaling
---[i]G-Protein linked cell surface receptor protein-mediated signaling
---[i]enzyme linked cell surface receptor protein-mediated signaling