Patterns of interactions of reaction pairs in metabolic networks

Jozsef Bruck, Oliver Ebenhoeh, Reinhart Heinrich

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

A large scale structural analysis of metabolic networks is presented focusing on neighbourhood relationships between individual reactions. We define two reactions to be neighbored if one of them provides the necessary set of substances for the other to proceed. A method is developed which allows determining all possible neighborhood relationships categorized as interaction patterns. These patterns differ in the types of participating reactions and in the way they share their reactants. The method is applied to a set of 4795 metabolic reactions contained in the KEGG database. We show that from the 1547 theoretically possible types of interactions 282 patterns are found in metabolism. More than 55% of all interactions occur between reactions with at most two reactants on one side. In these interactions only 25 different patterns play a role. We propose to use these neighborhood relationships as a concept of adjacency in large scale graph theoretical analyses of metabolism.
Original languageEnglish
Pages (from-to)208-218
Number of pages11
JournalGenome Informatics
Volume17
Issue number1
Publication statusPublished - 2006

Fingerprint

Metabolic Networks and Pathways
Databases

Keywords

  • Databases, Factual
  • Glucokinase
  • Metabolic Networks and Pathways
  • Phosphotransferases
  • Protein Interaction Mapping
  • Substrate Specificity

Cite this

Bruck, J., Ebenhoeh, O., & Heinrich, R. (2006). Patterns of interactions of reaction pairs in metabolic networks. Genome Informatics, 17(1), 208-218.

Patterns of interactions of reaction pairs in metabolic networks. / Bruck, Jozsef; Ebenhoeh, Oliver; Heinrich, Reinhart.

In: Genome Informatics, Vol. 17, No. 1, 2006, p. 208-218.

Research output: Contribution to journalArticle

Bruck, J, Ebenhoeh, O & Heinrich, R 2006, 'Patterns of interactions of reaction pairs in metabolic networks', Genome Informatics, vol. 17, no. 1, pp. 208-218.
Bruck J, Ebenhoeh O, Heinrich R. Patterns of interactions of reaction pairs in metabolic networks. Genome Informatics. 2006;17(1):208-218.
Bruck, Jozsef ; Ebenhoeh, Oliver ; Heinrich, Reinhart. / Patterns of interactions of reaction pairs in metabolic networks. In: Genome Informatics. 2006 ; Vol. 17, No. 1. pp. 208-218.
@article{dfa1dc5a9f7b4a0b9e2f1607067d5b42,
title = "Patterns of interactions of reaction pairs in metabolic networks",
abstract = "A large scale structural analysis of metabolic networks is presented focusing on neighbourhood relationships between individual reactions. We define two reactions to be neighbored if one of them provides the necessary set of substances for the other to proceed. A method is developed which allows determining all possible neighborhood relationships categorized as interaction patterns. These patterns differ in the types of participating reactions and in the way they share their reactants. The method is applied to a set of 4795 metabolic reactions contained in the KEGG database. We show that from the 1547 theoretically possible types of interactions 282 patterns are found in metabolism. More than 55{\%} of all interactions occur between reactions with at most two reactants on one side. In these interactions only 25 different patterns play a role. We propose to use these neighborhood relationships as a concept of adjacency in large scale graph theoretical analyses of metabolism.",
keywords = "Databases, Factual, Glucokinase, Metabolic Networks and Pathways, Phosphotransferases, Protein Interaction Mapping, Substrate Specificity",
author = "Jozsef Bruck and Oliver Ebenhoeh and Reinhart Heinrich",
year = "2006",
language = "English",
volume = "17",
pages = "208--218",
journal = "Genome Informatics",
issn = "0919-9454",
publisher = "Universal Academy Press",
number = "1",

}

TY - JOUR

T1 - Patterns of interactions of reaction pairs in metabolic networks

AU - Bruck, Jozsef

AU - Ebenhoeh, Oliver

AU - Heinrich, Reinhart

PY - 2006

Y1 - 2006

N2 - A large scale structural analysis of metabolic networks is presented focusing on neighbourhood relationships between individual reactions. We define two reactions to be neighbored if one of them provides the necessary set of substances for the other to proceed. A method is developed which allows determining all possible neighborhood relationships categorized as interaction patterns. These patterns differ in the types of participating reactions and in the way they share their reactants. The method is applied to a set of 4795 metabolic reactions contained in the KEGG database. We show that from the 1547 theoretically possible types of interactions 282 patterns are found in metabolism. More than 55% of all interactions occur between reactions with at most two reactants on one side. In these interactions only 25 different patterns play a role. We propose to use these neighborhood relationships as a concept of adjacency in large scale graph theoretical analyses of metabolism.

AB - A large scale structural analysis of metabolic networks is presented focusing on neighbourhood relationships between individual reactions. We define two reactions to be neighbored if one of them provides the necessary set of substances for the other to proceed. A method is developed which allows determining all possible neighborhood relationships categorized as interaction patterns. These patterns differ in the types of participating reactions and in the way they share their reactants. The method is applied to a set of 4795 metabolic reactions contained in the KEGG database. We show that from the 1547 theoretically possible types of interactions 282 patterns are found in metabolism. More than 55% of all interactions occur between reactions with at most two reactants on one side. In these interactions only 25 different patterns play a role. We propose to use these neighborhood relationships as a concept of adjacency in large scale graph theoretical analyses of metabolism.

KW - Databases, Factual

KW - Glucokinase

KW - Metabolic Networks and Pathways

KW - Phosphotransferases

KW - Protein Interaction Mapping

KW - Substrate Specificity

M3 - Article

VL - 17

SP - 208

EP - 218

JO - Genome Informatics

JF - Genome Informatics

SN - 0919-9454

IS - 1

ER -