Reconstructing Phylogeny by Aligning Multiple Metabolic Pathways Using Functional Module Mapping.
Reconstructing Phylogeny by Aligning Multiple Metabolic Pathways Using Functional Module Mapping.
复制标题
使用功能模块映射对齐多个代谢途径来重建系统发育
DOI：
10.3390/molecules23020486
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发表时间：
2018-02-23
期刊：
影响因子：
--
通讯作者：
Peng Y
中科院分区：
文献类型：
--
作者：
Huang Y;Zhong C;Lin HX;Wang J;Peng Y
Comparison of metabolic pathways provides a systematic way for understanding the evolutionary and phylogenetic relationships in systems biology. Although a number of phylogenetic methods have been developed, few efforts have been made to provide a unified phylogenetic framework that sufficiently reflects the metabolic features of organisms. In this paper, we propose a phylogenetic framework that characterizes the metabolic features of organisms by aligning multiple metabolic pathways using functional module mapping. Our method transforms the alignment of multiple metabolic pathways into constructing the union graph of pathways, builds mappings between functional modules of pathways in the union graph, and infers phylogenetic relationships among organisms based on module mappings. Experimental results show that the use of functional module mapping enables us to correctly categorize organisms into main categories with specific metabolic characteristics. Traditional genome-based phylogenetic methods can reconstruct phylogenetic relationships, whereas our method can offer in-depth metabolic analysis for phylogenetic reconstruction, which can add insights into traditional phyletic reconstruction. The results also demonstrate that our phylogenetic trees are closer to the classic classifications in comparison to existing classification methods using metabolic pathway data.
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影响因子：
5.8
作者：
Clemente, Jose C.;Satou, Kenji;Valiente, Gabriel
通讯作者：
Valiente, Gabriel
Isorankn：多个蛋白质网络全局对齐的光谱方法。
DOI：
10.1093/bioinformatics/btp203
发表时间：
2009-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
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通讯作者：
Berger B
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作者：
Alberich R;Llabrés M;Sánchez D;Simeoni M;Tuduri M
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影响因子：
3
作者：
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通讯作者：
Ekker SC
影响因子：
3.7
作者：
Huang Y;Zhong C;Lin HX;Huang J
通讯作者：
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