Using the web interface, over-representation analysis can be carried out with gene sets and functional modules derived from two methods. The first method incorporates pathway definitions as given by the source databases. The second method is based on functional modules defined by proximity measures using the integrated network structure. It includes a node (for example a gene) as the module centre and its neighbours within a user-specified interaction proximity radius. For example, modules with radius 1 include the central gene and all its direct neighbors (genes that appear in a functional interaction together with the central one), and modules with radius 2 additionally include the neighbours of the neighbours of the central gene. Moreover, interconnectivity of module members can be specified by the user with the clustering index. For each predefined module, a P-value is calculated based on the hypergeometric distribution. The P-value reflects the significance of the observed overlap between the input gene list and the module's members as compared to random expectations. A small P-value indicates that more of the module's members are present in the input list
