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A computational method using the random walk with restart algorithm for identifying novel epigenetic factors

文献类型：期刊论文

作者Li, JiaRui1; Wang, ShaoPeng1; Cai, Yu-Dong1; Chen, Lei3; Zhang, YuHang2; Kong, XiangYin2; Huang, Tao2; ,
刊名MOLECULAR GENETICS AND GENOMICS
出版日期2018
卷号293期号:1页码:293-301
关键词Epigenetic regulation Epigenetic factor Random walk with restart Protein-protein interaction network
ISSN号1617-4615
DOI10.1007/s00438-017-1374-5
文献子类Article
英文摘要Epigenetic regulation has long been recognized as a significant factor in various biological processes, such as development, transcriptional regulation, spermatogenesis, and chromosome stabilization. Epigenetic alterations lead to many human diseases, including cancer, depression, autism, and immune system defects. Although efforts have been made to identify epigenetic regulators, it remains a challenge to systematically uncover all the components of the epigenetic regulation in the genome level using experimental approaches. The advances of constructing protein-protein interaction (PPI) networks provide an excellent opportunity to identify novel epigenetic factors computationally in the genome level. In this study, we identified potential epigenetic factors by using a computational method that applied the random walk with restart (RWR) algorithm on a protein-protein interaction (PPI) network using reported epigenetic factors as seed nodes. False positives were identified by their specific roles in the PPI network or by a low-confidence interaction and a weak functional relationship with epigenetic regulators. After filtering out the false positives, 26 candidate epigenetic factors were finally accessed. According to previous studies, 22 of these are thought to be involved in epigenetic regulation, suggesting the robustness of our method. Our study provides a novel computational approach which successfully identified 26 potential epigenetic factors, paving the way on deepening our understandings on the epigenetic mechanism.
学科主题Biochemistry & Molecular Biology ; Genetics & Heredity
WOS关键词HISTONE ACETYLTRANSFERASE ; SEQUENCE SPECIFICITY ; PROTEIN INTERACTIONS ; CHROMATIN-STRUCTURE ; DNA ; GENES ; IDENTIFICATION ; CELLS ; DEMETHYLATION ; TRANSCRIPTION
语种英语
WOS记录号WOS:000423833400025
出版者SPRINGER HEIDELBERG
版本出版稿
源URL[http://202.127.25.144/handle/331004/621]  
专题中国科学院上海生命科学研究院营养科学研究所
作者单位1.Shanghai Univ, Sch Life Sci, Shanghai 200444, Peoples R China;
2.Univ Chinese Acad Sci, Shanghai Inst Biol Sci, Chinese Acad Sci, Inst Hlth Sci, Shanghai 200031, Peoples R China,
3.Shanghai Maritime Univ, Coll Informat Engn, Shanghai 201306, Peoples R China;
推荐引用方式
GB/T 7714		 Li, JiaRui,Wang, ShaoPeng,Cai, Yu-Dong,et al. A computational method using the random walk with restart algorithm for identifying novel epigenetic factors[J]. MOLECULAR GENETICS AND GENOMICS,2018,293(1):293-301.
APA Li, JiaRui.,Wang, ShaoPeng.,Cai, Yu-Dong.,Chen, Lei.,Zhang, YuHang.,...&,.(2018).A computational method using the random walk with restart algorithm for identifying novel epigenetic factors.MOLECULAR GENETICS AND GENOMICS,293(1),293-301.
MLA Li, JiaRui,et al."A computational method using the random walk with restart algorithm for identifying novel epigenetic factors".MOLECULAR GENETICS AND GENOMICS 293.1(2018):293-301.

入库方式： OAI收割

来源：上海营养与健康研究所

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