Adding new members to the network and assocaited analyses.

When adding a new ligand/receptor mediated pathway, you will need to update the following files at a minimum: networkXXX.sif

• add the ligand (GENE1) and receptor (GENE2), as well as any downfield node that the latter controls (GENE3) GENE1 up-regulates GENE2 GENE2 up-regulates GENE3

receptorlist.txt

• add receptor GENE2

ligandlist.yaml

• add receptor/ligand pair GENE2: [GENE1]

Notes

• Use Alpha numerical characters only! (PLCB, not PLCβ)
• Only use GENE name, not protein name (G proteins are named as complexes right now, e.g. Gai, but need to figure this out later).
• When adding nodes, one of the intermediaries needs to connect to a preexisting part of the network
• search for names that are already in the list (such as CXCR4) to ensure you’re not adding duplicate entries
• Be very careful about the order (CXCR4 upreg Gai, not Gai upreg CXCR4)
• Double check pathways you’ve added in cytoscape to make sure they’re consistent with KEGG, etc
• Make sure all entries are connected to a preexisting node in the network