Fig. 1

Function prediction procedures in network biology. Network-based prediction methods of protein function are described schematically. There are two approaches to explore function from network in biology, direct and module-assisted methods. In the direct method which is not our subject in this study, the annotation of gene/protein neighbors are used to predict function. But in the module-assisted methods, node’s community/neighborhood is principal for function prediction. These methods are also divided into two categories i.e. graph and distance-based clustering methods. The validation is the main step after finding modules in the PPIN or using direct methods. Any assignment of function based on annotation of neighbors or neighborhood should be evaluated by the different validating methods. We introduce the IPN-based validation for this purpose