Prediction and characterization of protein-protein interaction networks in swine

KIZ OpenIR > 结构生物信息学

	Prediction and characterization of protein-protein interaction networks in swine
	Wang F 1; Liu MX 1; Song BX 2; Li DY 2; Pei HM 3; Guo Y 1; Huang JF4; Zhang DL2; huangjf@mail.kiz.ac.cn ; zhangdeli@tsinghua.org.cn
	2012
发表期刊	PROTEOME SCIENCE
卷号	10 期号:x 页码:2
合作性质	其它
摘要	Background: Studying the large-scale protein-protein interaction (PPI) network is important in understanding biological processes. The current research presents the first PPI map of swine, which aims to give new insights into understanding their biological processes. Results: We used three methods, Interolog-based prediction of porcine PPI network, domain-motif interactions from structural topology-based prediction of porcine PPI network and motif-motif interactions from structural topology-based prediction of porcine PPI network, to predict porcine protein interactions among 25,767 porcine proteins. We predicted 20,213, 331,484, and 218,705 porcine PPIs respectively, merged the three results into 567,441 PPIs, constructed four PPI networks, and analyzed the topological properties of the porcine PPI networks. Our predictions were validated with Pfam domain annotations and GO annotations. Averages of 70, 10,495, and 863 interactions were related to the Pfam domain-interacting pairs in iPfam database. For comparison, randomized networks were generated, and averages of only 4.24, 66.79, and 44.26 interactions were associated with Pfam domain-interacting pairs in iPfam database. In GO annotations, we found 52.68%, 75.54%, 27.20% of the predicted PPIs sharing GO terms respectively. However, the number of PPI pairs sharing GO terms in the 10,000 randomized networks reached 52.68%, 75.54%, 27.20% is 0. Finally, we determined the accuracy and precision of the methods. The methods yielded accuracies of 0.92, 0.53, and 0.50 at precisions of about 0.93, 0.74, and 0.75, respectively. Conclusion: The results reveal that the predicted PPI networks are considerably reliable. The present research is an important pioneering work on protein function research. The porcine PPI data set, the confidence score of each interaction and a list of related data are available at (http://pppid.biositemap.com/).
关键词	Protein-protein Interaction Network Interolog D-mist
资助者	The present work was supported by Kunming Institute of Zoology, Chinese Academy of Sciences (Grant NO. Y002731071) and grants from the National Natural Science Foundations of China (Grant NO. 31072115). ; The present work was supported by Kunming Institute of Zoology, Chinese Academy of Sciences (Grant NO. Y002731071) and grants from the National Natural Science Foundations of China (Grant NO. 31072115). ; The present work was supported by Kunming Institute of Zoology, Chinese Academy of Sciences (Grant NO. Y002731071) and grants from the National Natural Science Foundations of China (Grant NO. 31072115). ; The present work was supported by Kunming Institute of Zoology, Chinese Academy of Sciences (Grant NO. Y002731071) and grants from the National Natural Science Foundations of China (Grant NO. 31072115).
收录类别	SCI
语种	英语
资助者	The present work was supported by Kunming Institute of Zoology, Chinese Academy of Sciences (Grant NO. Y002731071) and grants from the National Natural Science Foundations of China (Grant NO. 31072115). ; The present work was supported by Kunming Institute of Zoology, Chinese Academy of Sciences (Grant NO. Y002731071) and grants from the National Natural Science Foundations of China (Grant NO. 31072115). ; The present work was supported by Kunming Institute of Zoology, Chinese Academy of Sciences (Grant NO. Y002731071) and grants from the National Natural Science Foundations of China (Grant NO. 31072115). ; The present work was supported by Kunming Institute of Zoology, Chinese Academy of Sciences (Grant NO. Y002731071) and grants from the National Natural Science Foundations of China (Grant NO. 31072115).
WOS记录号	WOS:000301709000002
引用统计	被引频次：23[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/6924
专题	结构生物信息学遗传资源与进化国家重点实验室
通讯作者	huangjf@mail.kiz.ac.cn; zhangdeli@tsinghua.org.cn
作者单位	1.College of Life Science, Center for Bioinformatics, Northwest A&F University, Yangling, Shaanxi 712100, China 2.College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China 3.College of forestry, Northwest A&F University, Yangling, Shaanxi 712100, 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,Liu MX,Song BX,et al. Prediction and characterization of protein-protein interaction networks in swine[J]. PROTEOME SCIENCE,2012,10(x):2.
APA	Wang F.,Liu MX.,Song BX.,Li DY.,Pei HM.,...&zhangdeli@tsinghua.org.cn.(2012).Prediction and characterization of protein-protein interaction networks in swine.PROTEOME SCIENCE,10(x),2.
MLA	Wang F,et al."Prediction and characterization of protein-protein interaction networks in swine".PROTEOME SCIENCE 10.x(2012):2.

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