Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs

doi:10.1186/1471-2105-13-S7-S6

CSpace > 应用数学研究所

	Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs
	Liu,Zhi-Ping 1,2; Wang,Jiguang 1,3; Qiu,Yu-Qing 4; Leung,Ross KK 5; Zhang,Xiang-Sun2,4 ; Tsui,Stephen KW 5; Chen,Luonan 1,2,6
	2012-05-08
发表期刊	BMC Bioinformatics
ISSN	1471-2105
卷号	13 期号:Suppl 7
摘要	AbstractBackgroundMycobacterium tuberculosis is an infectious bacterium posing serious threats to human health. Due to the difficulty in performing molecular biology experiments to detect protein interactions, reconstruction of a protein interaction map of M. tuberculosis by computational methods will provide crucial information to understand the biological processes in the pathogenic microorganism, as well as provide the framework upon which new therapeutic approaches can be developed.ResultsIn this paper, we constructed an integrated M. tuberculosis protein interaction network by machine learning and ortholog-based methods. Firstly, we built a support vector machine (SVM) method to infer the protein interactions of M. tuberculosis H37Rv by gene sequence information. We tested our predictors in Escherichia coli and mapped the genetic codon features underlying its protein interactions to M. tuberculosis. Moreover, the documented interactions of 14 other species were mapped to the interactome of M. tuberculosis by the interolog method. The ensemble protein interactions were validated by various functional relationships, i.e., gene coexpression, evolutionary relationship and functional similarity, extracted from heterogeneous data sources. The accuracy and validation demonstrate the effectiveness and efficiency of our framework.ConclusionsA protein interaction map of M. tuberculosis is inferred from genetic codons and interologs. The prediction accuracy and numerically experimental validation demonstrate the effectiveness and efficiency of our method. Furthermore, our methods can be straightforwardly extended to infer the protein interactions of other bacterial species.
DOI	10.1186/1471-2105-13-S7-S6
语种	英语
WOS记录号	BMC:10.1186/1471-2105-13-S7-S6
出版者	BioMed Central
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/197
专题	应用数学研究所
通讯作者	Liu,Zhi-Ping; Chen,Luonan
作者单位	1.Chinese Academy of Sciences; Key Laboratory of Systems Biology, SIBS-Novo Nordisk Translational Research Centre for PreDiabetes, Shanghai Institutes for Biological Sciences 2.Chinese Academy of Sciences; National Center for Mathematics and Interdisciplinary Sciences 3.Chinese Academy of Sciences; Beijing Institute of Genomics 4.Chinese Academy of Sciences; Academy of Mathematics and Systems Science 5.The Chinese University of Hong Kong, Shatin N. T.; Hong Kong Bioinformatics Centre, School of Biomedical Sciences 6.University of Tokyo; Collaborative Research Center for Innovative Mathematical Modelling, Institute of Industrial Science
推荐引用方式 GB/T 7714	Liu,Zhi-Ping,Wang,Jiguang,Qiu,Yu-Qing,et al. Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs[J]. BMC Bioinformatics,2012,13(Suppl 7).
APA	Liu,Zhi-Ping.,Wang,Jiguang.,Qiu,Yu-Qing.,Leung,Ross KK.,Zhang,Xiang-Sun.,...&Chen,Luonan.(2012).Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs.BMC Bioinformatics,13(Suppl 7).
MLA	Liu,Zhi-Ping,et al."Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs".BMC Bioinformatics 13.Suppl 7(2012).