Institute of Computing Technology, Chinese Academy IR
Phylophenetic properties of metabolic pathway topologies as revealed by global analysis | |
Zhang, Y; Li, SJ; Skogerbo, G; Zhang, ZH; Zhu, XP; Zhang, ZF; Sun, SW; Lu, HC; Shi, BC; Chen, RS | |
2006-05-09 | |
发表期刊 | BMC BIOINFORMATICS |
ISSN | 1471-2105 |
卷号 | 7页码:13 |
摘要 | Background: As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. In the post-genomic era, it is possible to measure the "phylophenetic" contents of different pathways topologies from a global perspective. Results: We reconstructed phylophenetic trees for all available metabolic pathways based on topological similarities, and compared them to the corresponding 16S rRNA-based trees. Similarity values for each pair of trees ranged from 0.044 to 0.297. Using the quartet method, single pathways trees were merged into a comprehensive tree containing information from a large part of the entire metabolic networks. This tree showed considerably higher similarity (0.386) to the corresponding 16S rRNA-based tree than any tree based on a single pathway, but was, on the other hand, sufficiently distinct to preserve unique phylogenetic information not reflected by the 16S rRNA tree. Conclusion: We observed that the topology of different metabolic pathways provided different phylogenetic and phenetic information, depicting the compromise between phylogenetic information and varying evolutionary pressures forming metabolic pathway topologies in different organisms. The phylogenetic information content of the comprehensive tree is substantially higher than that of any tree based on a single pathway, which also gave clues to constraints working on the topology of the global metabolic networks, information that is only partly reflected by the topologies of individual metabolic pathways. |
DOI | 10.1186/1471-2105-7-252 |
收录类别 | SCI |
语种 | 英语 |
WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology |
WOS类目 | Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology |
WOS记录号 | WOS:000238647700001 |
出版者 | BIOMED CENTRAL LTD |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | http://119.78.100.204/handle/2XEOYT63/10541 |
专题 | 中国科学院计算技术研究所期刊论文_英文 |
通讯作者 | Chen, RS |
作者单位 | 1.Chinese Acad Sci, Bioinformat Lab & Natl Lab Bromacromol, Inst Biophys, Beijing 100101, Peoples R China 2.Inst Comp Technol, Bioinformat Res Grp, Key Lab Intelligent Informat Proc, Beijing 100080, Peoples R China 3.Chinese Acad Sci, Grad Sch, Beijing, Peoples R China |
推荐引用方式 GB/T 7714 | Zhang, Y,Li, SJ,Skogerbo, G,et al. Phylophenetic properties of metabolic pathway topologies as revealed by global analysis[J]. BMC BIOINFORMATICS,2006,7:13. |
APA | Zhang, Y.,Li, SJ.,Skogerbo, G.,Zhang, ZH.,Zhu, XP.,...&Chen, RS.(2006).Phylophenetic properties of metabolic pathway topologies as revealed by global analysis.BMC BIOINFORMATICS,7,13. |
MLA | Zhang, Y,et al."Phylophenetic properties of metabolic pathway topologies as revealed by global analysis".BMC BIOINFORMATICS 7(2006):13. |
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