Annotating ligand-receptor pathways

 TO BE REVIEWED 

General ligand-receptor pathway

Stimulus

• regulation of signaling pathway

Ligand

• signaling pathway
• regulation of other cellular processes

Receptor

• signaling pathway
• regulation of other cellular processes

Signaling molecules

• signaling pathway
• regulation of other process(es)
• regulation of gene-specific transcription
• regulation of translation
• (regulation of) transcription in response to stimulus ligand
• (regulation of) transcription involved in other process(es)
• (regulation of ) other cellular process(es)

Transcription factors*

• signaling pathway
• regulation of transcription involved in other process(es)

Target

• cellular response to stimulus
• other process(es)
• regulation of other processes

• We would not consider annotating the core transcription machinery to the downstream (other) processes that the target is involved in unless the transcription factor is gene-specific, in which case we would annotate to regulation of transcription involved in other process(es)

   Regulation of glucose transport
   

Insulin (ligand)

• insulin receptor signaling pathway
• regulation of glucose transport/homeostasis

Insulin receptor (receptor)

• Insulin receptor signaling pathway
• Regulation of glucose transport/homeostasis

IRS1, PI3K, PDK1, PKC (signaling molecules)

• Insulin receptor signaling pathway
• Regulation of glucose transport/homeostasis
• Protein localization at cell surface (NTR: involved in response to insulin)

GLUT4 (target)

• Cellular response to insulin
• Glucose transport/homeostasis