TY - JOUR
T1 - Reconstructing phylogeny by aligning multiple metabolic pathways using functional module mapping
AU - Huang, Yiran
AU - Zhong, Cheng
AU - Lin, Hai Xiang
AU - Wang, Jianyi
AU - Peng, Yuzhong
PY - 2018
Y1 - 2018
N2 - 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.
AB - 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.
KW - Functional module mapping
KW - Metabolic pathway alignment
KW - Phylogenetic tree
KW - Union graph
UR - http://resolver.tudelft.nl/uuid:bb1d09e5-9a11-4db2-9d37-2338778e232e
UR - http://www.scopus.com/inward/record.url?scp=85042397550&partnerID=8YFLogxK
U2 - 10.3390/molecules23020486
DO - 10.3390/molecules23020486
M3 - Article
AN - SCOPUS:85042397550
SN - 1420-3049
VL - 23
SP - 1
EP - 16
JO - Molecules: a journal of synthetic organic and natural product chemistry
JF - Molecules: a journal of synthetic organic and natural product chemistry
IS - 2
M1 - 486
ER -