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In this study, a novel method of structure analysis of probabilistic Boolean network (PBN) is represented. According to the influence matrix of PBN, essential genes can be found the rules given. Setting these genes as source nodes, by using shortest path search and maximum information passing, PBN can be decomposed into several sub-networks. This algorithm is illustrated using an artificial influenced-based network and an example of influences in a small network with glioma data.