Signaling ontology structure documentation
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[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