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题名:
Combining sequence and Gene Ontology for protein module detection in the Weighted Network
作者: Yu, Yang; Liu, Jie; Feng, Nuan; Song Bo(宋立波); Zheng ZY(郑泽宇)
作者部门: 数字工厂研究室
通讯作者: Yu, Yang ; Feng, Nuan
关键词: Protein complex ; Protein interaction ; Gene Ontology ; The Weighted Network
刊名: JOURNAL OF THEORETICAL BIOLOGY
ISSN号: 0022-5193
出版日期: 2017
卷号: 412, 页码:107-112
收录类别: SCI
产权排序: 1
项目资助者: 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记录号: WOS:000391081500012
WOS标题词: Science & Technology ; Life Sciences & Biomedicine
类目[WOS]: Biology ; Mathematical & Computational Biology
关键词[WOS]: SEMANTIC SIMILARITY ; COMPLEXES ; INFORMATION ; ALGORITHM ; MODULARITY ; CASCADE ; CANCER ; TERMS ; YEAST
研究领域[WOS]: Life Sciences & Biomedicine - Other Topics ; Mathematical & Computational Biology
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内容类型: 期刊论文
URI标识: http://ir.sia.cn/handle/173321/19823
Appears in Collections:数字工厂研究室_期刊论文

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Recommended Citation:
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.
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文件名: Combining sequence and Gene Ontology for protein module detection in the Weighted Network.pdf
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