Jian Gao, Bin Hu and Lei Chen*
Background: Identification of protein phenotypic annotations is an essential and challenging problem in modern genetics. Such problem is related to some serious diseases, including cancers, HIV and so on. The factors of genotype and environment increase the difficulties in determining the phenotype of proteins. The experiment methods to achieve such a goal are always time-consuming and expensive.
Objective: The aim of this study was to design a quick and cheap method for determining the phenotypes of proteins.
Method: In this study, we proposed a network computational method to identify novel phenotypic annotations of proteins. To execute such a method, a heterogeneous network was constructed, which contained three sub-networks: protein network, phenotypic type network, and protein-phenotypic type network. The method tried to find out all paths with limited length, which connected one protein and one phenotypic type. A scoring scheme was adopted to count obtained paths and generate a score to indicate the associations between them.
Results and Conclusion: The ROC and PR curve analyses were done to evaluate the performance of the method, indicating the utility of the method. Our method was found to be superior to other network methods, which incorporated popular network algorithms.
Protein, phenotype, heterogeneous network, protein-protein interaction, path, Jackknife test.
College of Information Engineering, Shanghai Maritime University, Shanghai 201306, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, College of Information Engineering, Shanghai Maritime University, Shanghai 201306