title: Connectivity matrix method for analyses of biological networks and its application to atom-level analysis of a model network of carbohydrate metabolism.
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, intermetabolite 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.
authors.affiliation: Global Health and Environmental Sciences, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikatacho, Okayama 700-8558, Japan. jo25@md.okayama-u.ac.jp
authors.forename: J
authors.initials: J
authors.lastname: Ohta
mesh_terms: D000222:Adaptation, Physiological / Q000502:physiology; D000465:Algorithms; D000818:Animals; D050260:Carbohydrate Metabolism / Q000502:physiology*; D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D005246:Feedback / Q000502:physiology; D006706:Homeostasis / Q000502:physiology; D006801:Humans; D007700:Kinetics; D008954:Models, Biological; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*
chemical_list: D020543:Proteome