Nucleic Acids Research Advance Access originally published online on October 16, 2007
Nucleic Acids Research 2007 35(20):e134; doi:10.1093/nar/gkm769
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Nucleic Acids Research, 2007, Vol. 35, No. 20 e134
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis
Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, 820-8502, Fukuoka, Japan
*To whom correspondence should be addressed. Tel: +81 948 29 7828; Fax: +81 948 29 7828; Email: kurata{at}bio.kyutech.ac.jp
Received May 24, 2007. Revised September 12, 2007. Accepted September 12, 2007.
Biochemical network maps are helpful for understanding the mechanism of how a collection of biochemical reactions generate particular functions within a cell. We developed a new and computationally feasible notation that enables drawing a wide resolution map from the domain-level reactions to phenomenological events and implemented it as the extended GUI network constructor of CADLIVE (Computer-Aided Design of LIVing systEms). The new notation presents ‘Domain expansion’ for proteins and RNAs, ‘Virtual reaction and nodes’ that are responsible for illustrating domain-based interaction and ‘InnerLink’ that links real complex nodes to virtual nodes to illustrate the exact components of the real complex. A modular box is also presented that packs related reactions as a module or a subnetwork, which gives CADLIVE a capability to draw biochemical maps in a hierarchical modular architecture. Furthermore, we developed a pathway search module for virtual knockout mutants as a built-in application of CADLIVE. This module analyzes gene function in the same way as molecular genetics, which simulates a change in mutant phenotypes or confirms the validity of the network map. The extended CADLIVE with the newly proposed notation is demonstrated to be feasible for computational simulation and analysis.
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