title: Combining sequence and Gene Ontology for protein module detection in the Weighted Network.
abstract: Studies of protein modules in a Protein-Protein Interaction (PPI) network contribute greatly to the understanding of biological mechanisms. With the development of computing science, computational approaches have played an important role in locating protein modules. In this paper, a new approach combining Gene Ontology and amino acid background frequency is introduced to detect the protein modules in the weighted PPI networks. The proposed approach mainly consists of three parts: the feature extraction, the weighted graph construction and the protein complex detection. Firstly, the topology-sequence information is utilized to present the feature of protein complex. Secondly, six types of the weighed graph are constructed by combining PPI network and Gene Ontology information. Lastly, protein complex algorithm is applied to the weighted graph, which locates the clusters based on three conditions, including density, network diameter and the included angle cosine. Experiments have been conducted on two protein complex benchmark sets for yeast and the results show that the approach is more effective compared to five typical algorithms with the performance of f-measure and precision. The combination of protein interaction network with sequence and gene ontology data is helpful to improve the performance and provide a optional method for protein module detection.
authors.affiliation: Software College, Shenyang Normal University, Shenyang 110034, PR China; Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, PR China. Electronic address: yuyangsd1204@126.com.
authors.forename: Yang
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Software College, Shenyang Normal University, Shenyang 110034, PR China.
authors.forename: Jie
authors.initials: J
authors.lastname: Liu
authors.affiliation: College of Information Technology, Shenyang Institute of Technology, Fushun 113122, PR China. Electronic address: 279901222@qq.com.
authors.forename: Nuan
authors.initials: N
authors.lastname: Feng
authors.affiliation: Software College, Shenyang Normal University, Shenyang 110034, PR China.
authors.forename: Bo
authors.initials: B
authors.lastname: Song
authors.affiliation: Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, PR China.
authors.forename: Zeyu
authors.initials: Z
authors.lastname: Zheng
mesh_terms: D063990:Gene Ontology; D011506:Proteins / Q000235:genetics*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D011506:Proteins
keywords: Gene Ontology; Protein complex; Protein interaction; The Weighted Network