How do I interpret the p-value of a module?

Let’s call the edges within a module “internal” and the edges connecting the nodes of a module with the rest of the graph “external”. The null hypothesis of the test is that there is no difference between the number of “internal” and “external” connections to a given node in the module. The p-value of a given module is calculated using a Wilcoxon rank-sum test of the “internal” and “external” degrees.

The p-value of a module is based solely on network connectivity, and gives some indication of how significant the connections within a defined module are. Users should also consider whether the modules are ‘active’ under the experimental conditions, by taking into account the number of seeds, their average fold changes (gene expression), as well as the enriched functions displayed in the Module Explorer table.

You may also want to read module detection algorithm.