Question: Finding clusters of interacting proteins in a protein-protein interaction graph
gravatar for rubic
3.1 years ago by
United States
rubic190 wrote:


Given a protein-protein-interaction graph (e.g., from the string data base) and an outcome of a differential expression analysis (i.e., for each gene we have its log fold-change and the associated p-value between the treatment and control), is there a graph-based algorithm that can find subgraph parts enriched with genes which log fold-change p-value is below a given cutoff?

ADD COMMENTlink modified 3.1 years ago by Diwan560 • written 3.1 years ago by rubic190
gravatar for Diwan
3.1 years ago by
United States
Diwan560 wrote:

Given a list of differentially expressed genes, 'keypathwayminer' in cytoscape can extract the highly connected sub-network from PPI. I had used their older version and found it helpful.

Check here for app:

Their recent paper:

To further group the sub-network, you can try 'clusterviz' app in cytoscape to get network clusters.

An application paper that uses both keypathwayminer and clusterviz:

ADD COMMENTlink written 3.1 years ago by Diwan560
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