Prediction and Analysis of the Protein-Protein Interaction Networks for Chickens, Cattle, Dogs, Horses and Rabbits

	Prediction and Analysis of the Protein-Protein Interaction Networks for Chickens, Cattle, Dogs, Horses and Rabbits
	Wang F 1; Song BX 2; Zhou N 2; Jiang PF 2; Sang Q 3; Huang JF 4; Zhang DL[*]1,2; Zhao X 2; Miao YT 2; Li DY 2
刊名	CURRENT BIOINFORMATICS
	2016
卷号	11 期号:1 页码:131-142
关键词	D-MIST Gene ontology annotations InParanoid protein-protein interaction subcellular localization
通讯作者	zhangdeli@tsinghua.org.cn
合作状况	其它
英文摘要	The development of high-throughput screening for protein-protein interaction (PPI) is currently utilized for detailed experimentation and the formulation of biological hypotheses. Comprehensive and concrete PPI networks of domestic animals are urgently needed because of their considerable economic value. We constructed the PPI networks of chickens, cattle, dogs, horses, and rabbits using the InParanoid method, an interolog method that depends on protein ortholog algorithms, and the domain-motif interactions from structural topology (D-MIST) method which is defined as if a motif in protein A matches a domain in protein B in the position-specific scoring matrices, protein A likely interacts with protein B. Up to 328,590 PPIs were found in chickens, 447,014 in cattle, 129,386 in dogs, 93,414 in horses and 115,296 in rabbits. Furthermore, a large number of novel PPIs with diverse biological roles were discovered. Gene ontology annotation and subcellular localization were applied to verify the results. In GO annotations, 30.28% to 50.08% and 35.32% to 39.97% of the predicted PPIs were found sharing GO terms using Inparanoid and D-MIST. In subcellular localization, 55.04% to 59.97% and 35.43% to 40.26% of the predicted PPIs had the same subcellular localization using Inparanoid and D-MIST. Compared with the randomized networks, the results revealed the predicted networks were considerably reliable. This work, to some extent establishes the biological significance of these PPI networks and provides clues to further decipher the molecular mechanism of circadian rhythmicity.
收录类别	SCI
资助信息	The present work was supported by the opening foundation of the State Key Laborarory of Genetic Resources and Evolution (GREKF12-03) and National Natural Science Foundations of China (Grant No. 31072115). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.
语种	英语
内容类型	期刊论文
源URL	[http://159.226.149.26:8080/handle/152453/10328]
专题	昆明动物研究所_结构生物信息学昆明动物研究所_遗传资源与进化国家重点实验室
作者单位	1.College of Life Science, Northwest A&F University and College of Life Science, Shanxi Agricultural University, Taigu 030800, Jinzhong, Shanxi, China 2.College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China 3.College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Xi’an, Shaanxi, P.R. China 4.State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, P.R. China
推荐引用方式 GB/T 7714	Wang F,Song BX,Zhou N,et al. Prediction and Analysis of the Protein-Protein Interaction Networks for Chickens, Cattle, Dogs, Horses and Rabbits[J]. CURRENT BIOINFORMATICS,2016,11(1):131-142.
APA	Wang F.,Song BX.,Zhou N.,Jiang PF.,Sang Q.,...&Li DY.(2016).Prediction and Analysis of the Protein-Protein Interaction Networks for Chickens, Cattle, Dogs, Horses and Rabbits.CURRENT BIOINFORMATICS,11(1),131-142.
MLA	Wang F,et al."Prediction and Analysis of the Protein-Protein Interaction Networks for Chickens, Cattle, Dogs, Horses and Rabbits".CURRENT BIOINFORMATICS 11.1(2016):131-142.