Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments

Yoshihiro Yamanishi, Yasuo Tabei, Masaaki Kotera

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Motivation: Recent advances in mass spectrometry and related metabolomics technologies have enabled the rapid and comprehensive analysis of numerous metabolites. However, biosynthetic and biodegradation pathways are only known for a small portion of metabolites, with most metabolic pathways remaining uncharacterized. Results: In this study, we developed a novel method for supervised de novo metabolic pathway reconstruction with an improved graph alignment-based approach in the reaction-filling framework. We proposed a novel chemical graph alignment algorithm, which we called PACHA (Pairwise Chemical Aligner), to detect the regioisomer-sensitive connectivities between the aligned substructures of two compounds. Unlike other existing graph alignment methods, PACHA can efficiently detect only one common subgraph between two compounds. Our results show that the proposed method outperforms previous descriptor-based methods or existing graph alignment-based methods in the enzymatic reaction-likeness prediction for isomer-enriched reactions. It is also useful for reaction annotation that assigns potential reaction characteristics such as EC (Enzyme Commission) numbers and PIERO (Enzymatic Reaction Ontology for Partial Information) terms to substrate-product pairs. Finally, we conducted a comprehensive enzymatic reaction-likeness prediction for all possible uncharacterized compound pairs, suggesting potential metabolic pathways for newly predicted substrate-product pairs.

Original languageEnglish
Pages (from-to)i161-i170
JournalBioinformatics
Volume31
Issue number12
DOIs
Publication statusPublished - Jun 15 2015

Fingerprint

Metabolome
Pathway
Alignment
Metabolic Networks and Pathways
Graph in graph theory
Metabolites
Substrates
Biodegradation
Pairwise
Metabolomics
Isomers
Biosynthetic Pathways
Mass spectrometry
Ontology
Substrate
Enzymes
Mass Spectrometry
Prediction
Partial Information
Substructure

All Science Journal Classification (ASJC) codes

  • Statistics and Probability
  • Medicine(all)
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments. / Yamanishi, Yoshihiro; Tabei, Yasuo; Kotera, Masaaki.

In: Bioinformatics, Vol. 31, No. 12, 15.06.2015, p. i161-i170.

Research output: Contribution to journalArticle

Yamanishi, Yoshihiro ; Tabei, Yasuo ; Kotera, Masaaki. / Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments. In: Bioinformatics. 2015 ; Vol. 31, No. 12. pp. i161-i170.
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