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	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
刊名	Bmc bioinformatics
	2006-05-09
卷号	7页码:13
ISSN号	1471-2105
DOI	10.1186/1471-2105-7-252
通讯作者	Chen, rs(crs@sun5.ibp.ac.cn)
英文摘要	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.
WOS关键词	PHYLOGENETIC ANALYSIS ; ESCHERICHIA-COLI ; SMALL-WORLD ; NETWORKS ; TREES ; ORGANISMS ; EVOLUTION ; RECONSTRUCTION ; ORGANIZATION ; ALIGNMENT
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
语种	英语
出版者	BIOMED CENTRAL LTD
WOS记录号	WOS:000238647700001
内容类型	期刊论文
URI标识	http://www.corc.org.cn/handle/1471x/2379088
专题	中国科学院大学
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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