Refine gene functional similarity network based on interaction networks

Background: In recent years, biological interaction networks have become the basis of some essential study and achieved success in many applications. Some typical networks such as protein-protein interaction networks have already been investigated systematically. However, little work has been available for the construction of gene functional similarity networks so far. In this research, we will try to build a high reliable gene functional similarity network to promote its further application. Results: Here, we propose a novel method to construct and refine the gene functional similarity network. It mainly contains three steps. First, we establish an integrated gene functional similarity networks based on different functional similarity calculation methods. Then, we construct a referenced gene-gene association network based on the protein-protein interaction networks. At last, we refine the spurious edges in the integrated gene functional similarity network with the help of the referenced gene-gene association network. Experiment results indicate that the refined gene functional similarity network (RGFSN) exhibits a scale-free, small world and modular architecture, with its degrees fit best to power law distribution. In addition, we conduct protein complex prediction experiment for human based on RGFSN and achieve an outstanding result, which implies it has high reliability and wide application significance. Conclusions: Our efforts are insightful for constructing and refining gene functional similarity networks, which can be applied to build other high quality biological networks.