KMS Of Academy of mathematics and systems sciences, CAS
| Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs | |
Liu,Zhi-Ping1,2; Wang,Jiguang1,3; Qiu,Yu-Qing4; Leung,Ross KK5; Zhang,Xiang-Sun2,4 ; Tsui,Stephen KW5; Chen,Luonan1,2,6
| |
| 2012-05-08 | |
| Source Publication | BMC Bioinformatics
 |
| ISSN | 1471-2105 |
| Volume | 13Issue:Suppl 7 |
| Abstract | 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 |
| Language | 英语 |
| WOS ID | BMC:10.1186/1471-2105-13-S7-S6 |
| Publisher | BioMed Central |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/197 |
| Collection | 应用数学研究所 |
| Corresponding Author | Liu,Zhi-Ping; Chen,Luonan |
| Affiliation | 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 |
| Recommended Citation 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). |
| Files in This Item: | There are no files associated with this item. | |||||
Items in the repository are protected by copyright, with all rights reserved, unless otherwise indicated.
Edit Comment