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Combining sequence and Gene Ontology for protein module detection in the Weighted Network
Yu, Yang; Liu, Jie; Feng, Nuan; Song, Bo; Zheng ZY(郑泽宇)
作者部门数字工厂研究室
关键词Protein Complex Protein Interaction Gene Ontology The Weighted Network
发表期刊JOURNAL OF THEORETICAL BIOLOGY
ISSN0022-5193
2017
卷号412页码:107-112
收录类别SCI
WOS记录号WOS:000391081500012
产权排序1
资助机构Science Research Project of Liaoning Province Education Department [L2015496, L201605] ; One-hundred Talent Program of the Chinese Academy of Sciences [Y5AA100A01]
摘要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.
语种英语
WOS标题词Science & Technology ; Life Sciences & Biomedicine
WOS类目Biology ; Mathematical & Computational Biology
关键词[WOS]SEMANTIC SIMILARITY ; COMPLEXES ; INFORMATION ; ALGORITHM ; MODULARITY ; CASCADE ; CANCER ; TERMS ; YEAST
WOS研究方向Life Sciences & Biomedicine - Other Topics ; Mathematical & Computational Biology
引用统计
文献类型期刊论文
条目标识符http://ir.sia.cn/handle/173321/19823
专题数字工厂研究室
通讯作者Yu, Yang; Feng, Nuan
作者单位1.Software College, Shenyang Normal University, Shenyang 110034, PR China
2.Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, PR China
3.College of Information Technology, Shenyang Institute of Technology, Fushun 113122, PR China
推荐引用方式
GB/T 7714
Yu, Yang,Liu, Jie,Feng, Nuan,et al. Combining sequence and Gene Ontology for protein module detection in the Weighted Network[J]. JOURNAL OF THEORETICAL BIOLOGY,2017,412:107-112.
APA Yu, Yang,Liu, Jie,Feng, Nuan,Song, Bo,&Zheng ZY.(2017).Combining sequence and Gene Ontology for protein module detection in the Weighted Network.JOURNAL OF THEORETICAL BIOLOGY,412,107-112.
MLA Yu, Yang,et al."Combining sequence and Gene Ontology for protein module detection in the Weighted Network".JOURNAL OF THEORETICAL BIOLOGY 412(2017):107-112.
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