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
1 answer
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!
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