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thpar / diffany

Diffany is an open-source toolbox for calculating and visualizing differential networks.
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[CLOSED] filter PPI hubs #192

Closed diffany-admin closed 9 years ago

diffany-admin commented 9 years ago

Issue by svlandeg Tue Sep 9 20:56:22 2014

Refine #182: PPI neighbours: exclude hubs? occurrence/percentage threshold?

diffany-admin commented 9 years ago

Comment by svlandeg Wed Sep 10 16:26:18 2014

NetworkAnalysis: 17778/66404 = 26.0% edges for 7240/7936 = 91.0% nodes 24064/66404 = 36.0% edges for 7596/7936 = 95.0% nodes 30320/66404 = 45.0% edges for 7778/7936 = 98.0% nodes

If we thus define the 340 most connected genes as hubs, we remove 64% edges. Or remove the 158 most connected ones and remove 55% of all edges

diffany-admin commented 9 years ago

Comment by svlandeg Thu Sep 11 10:16:25 2014

this method works, but I wonder whether it's sufficient. In the 1.5h (pairwise) comparison we still have these PPI "fans" around ARGOS, MPK3, ARL, etc. Do we need more custom filtering to elucidate actual pathways?!

diffany-admin commented 9 years ago

Comment by svlandeg Fri Sep 12 08:24:02 2014

this now seems to be largely fixed, e.g. for ARGOS and ARL, but MPK3 still has 25 neighbours?!