title: Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis.
abstract: 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.
authors.affiliation: Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, 820-8502, Fukuoka, Japan. kurata@bio.kyutech.ac.jp
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Kurata
authors.forename: Kentaro
authors.initials: K
authors.lastname: Inoue
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Maeda
authors.forename: Koichi
authors.initials: K
authors.lastname: Masaki
authors.forename: Yuki
authors.initials: Y
authors.lastname: Shimokawa
authors.forename: Quanyu
authors.initials: Q
authors.lastname: Zhao
mesh_terms: D000818:Animals; D003198:Computer Simulation; D008322:Mammals; D053858:Metabolic Networks and Pathways; D014176:Protein Biosynthesis; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D012984:Software; D016159:Tumor Suppressor Protein p53 / Q000378:metabolism
chemical_list: D011506:Proteins; D016159:Tumor Suppressor Protein p53; D012313:RNA