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We have constructed protein networks of kinome and cell cycle from MIPS database. The networks show character of scale free network, in which a few highly connected proteins play a central role in most cells. Protein-protein interaction database obtained from a yeast two hybrid screen or a composite data set includes random false positives. To purify the database, we employed cellular localization and DNA expression profile and then reconstructed kinome and cell cycle networks. The kinome and cell cycle networks constructed from the purified database show characters of scale free network and hierarchical network, in which preserves it's scale-free organization and displays inherent modularity of protein clusters. To find functional modules from the network, we propose a new technique that is based on multi-body correlations in kinome or cell cycle network. From the derived modules, we predicted and estimated tentative functions for unannotated proteins with high certainty.