How to find p-value in Cytoscape in network analysis?

Question

[Sky]

Hello everyone, I am new to bioinformatics and I am making a PPI in Cytoscape. I have seen in research articles while explaining about PPI in results, they also wrote PPI enrichment p-value, an average node degree, an average local clustering coefficient, an expected number of edges. I have found the rest but i couldnt find the expected number of edges, and a GGI enrichment pvalue. Can someone please help me how can I find these. I have tried to search on YouTube and google but couldn't find. thanks in advance

Answer 1

[Scooter]

When they talk about "enrichment" it refers to the determining if the terms associated with a set of nodes are enriched, or over-represented that one would expect based on random chance. Generally, your nodes might be genes and the terms might be GO terms or pathways. Also note that the p-Value (or FDR) for enrichment is really a "node" feature rather than a network feature. You can calculate the enrichment of a set of genes by using a variety of tools, but within Cytoscape, I would recommend using the Enrichment Table (Tools->Enrichment Table->Perform Gene Enrichment).

Hope this helps!