title: Large-scale identification of human protein function using topological features of interaction network.
abstract: The annotation of protein function is a vital step to elucidate the essence of life at a molecular level, and it is also meritorious in biomedical and pharmaceutical industry. Developments of sequencing technology result in constant expansion of the gap between the number of the known sequences and their functions. Therefore, it is indispensable to develop a computational method for the annotation of protein function. Herein, a novel method is proposed to identify protein function based on the weighted human protein-protein interaction network and graph theory. The network topology features with local and global information are presented to characterise proteins. The minimum redundancy maximum relevance algorithm is used to select 227 optimized feature subsets and support vector machine technique is utilized to build the prediction models. The performance of current method is assessed through 10-fold cross-validation test, and the range of accuracies is from 67.63% to 100%. Comparing with other annotation methods, the proposed way possesses a 50% improvement in the predictive accuracy. Generally, such network topology features provide insights into the relationship between protein functions and network architectures. The source code of Matlab is freely available on request from the authors.
authors.affiliation: School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China.
authors.forename: Zhanchao
authors.initials: Z
authors.lastname: Li
authors.affiliation: School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China.
authors.forename: Zhiqing
authors.initials: Z
authors.lastname: Liu
authors.affiliation: School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China.
authors.forename: Wenqian
authors.initials: W
authors.lastname: Zhong
authors.affiliation: School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China.
authors.forename: Menghua
authors.initials: M
authors.lastname: Huang
authors.affiliation: School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
authors.forename: Na
authors.initials: N
authors.lastname: Wu
authors.affiliation: School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Guangzhou, 510006, People's Republic of China.
authors.forename: Yun
authors.initials: Y
authors.lastname: Xie
authors.affiliation: School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
authors.forename: Zong
authors.initials: Z
authors.lastname: Dai
authors.affiliation: SYSU-CMU Shunde International Joint Research Institute, Shunde, 528300, People's Republic of China.|School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
authors.forename: Xiaoyong
authors.initials: X
authors.lastname: Zou
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps; D020543:Proteome / Q000378:metabolism*
chemical_list: D020543:Proteome