Pathway work/Queries/Queries from Lindsay

What proteins or complexes can interact with protein or complex X?

Can X and Y interact?

• Rules about domain interactions and X has_part domain D assertions
• Location information (which cell types expressed in and where in call can be found)
• Post-translational modifications that are required for a protein/complex to become activated (eg can Y phosphorylate X at the right place or if X needs to be phosphorylated, can Y do that or can Y induce a conformational change in X that will expose its active site)

Basically, can two interact, and if yes, in the way necessary to confer a capability that allows the protein/complex to participate in another interaction

Receptor collaboration

• For two pathways, do they share molecules, are they active in the same cell types, etc
• For any combination of pathways, what are the possible outcomes of signaling, and is signaling through one likely to alter the outcome of signaling through another if the two signals happen close enough together in time
• Outcomes we are particularly interested in:
  • Change in gene/protein expression (cytokines, chemokines, receptors)
  • Migration
  • Proliferation
  • Apoptosis

Harder questions for future consideration (although the SNP stuff is pretty important for the grant)

• Can we infer homologous pathways?
• Can we link from a pathway to OMIM via the PRO links from proteins to OMIM?
• Can we link to SNP data? (are SNPs located in regulatory sites, “important” protein domains, active sites, etc)
• If we known SNP locations for a variety of inbred mouse strains, can we check to see which strain groups, grouped based on having a similar disease phenotype, have SNPs in genes that are part of the same pathway
• Can we identify contradictory experimental results, predict known results, or use the results to infer a model of mechanism