Connectivity matrix method for analyses of biological networks and its application to atom-level analysis of a model network of carbohydrate metabolism

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3 Citations (Scopus)

Abstract

An approach for analysis of biological networks is proposed. In this approach, named the connectivity matrix (CM) method, all the connectivities of interest are expressed in a matrix. Then, a variety of analyses are performed on GNU Octave or Matlab. Each node in the network is expressed as a row vector or numeral that carries information defining or characterising the node itself. Information about connectivity itself is also expressed as a row vector or numeral. Thus, connection of node n1 to node n2 through edge e is expressed as [n1, n2, e], a row vector formed by the combination of three row vectors or numerals, where n1, n2, and e indicate two different nodes and one connectivity, respectively. All the connectivities in any given network are expressed as a matrix, CM, each row of which corresponds to one connectivity. Using this CM method, inter-metabolite atom-level connectivity is investigated in a model metabolic network composed of the reactions for glycolysis, oxidative decarboxylation of pyruvate, citric acid cycle, pentose phosphate pathway and gluconeogenesis.

Original languageEnglish
Pages (from-to)372-374
Number of pages3
JournalIEE Proceedings: Systems Biology
Volume153
Issue number5
DOIs
Publication statusPublished - Sep 1 2006

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Medicine
  • Modelling and Simulation
  • Molecular Biology
  • Genetics
  • Cell Biology

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