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Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis.

Kurata H, Inoue K, Maeda K, Masaki K, Shimokawa Y, Zhao Q - Nucleic Acids Res. (2007)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, 820-8502, Fukuoka, Japan. kurata@bio.kyutech.ac.jp

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.

Show MeSH
Improved graphical notation for regulators and reactions. The previous version of CADLIVE was improved to make clear the type of reactions. The regulator arrows are colored. The arrows of ‘homo association and modification’ and ‘homo association and modification with stoichiometric changes’ are revised. The reaction of ‘Set Modified from transition state’ is newly added.
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Figure 1: Improved graphical notation for regulators and reactions. The previous version of CADLIVE was improved to make clear the type of reactions. The regulator arrows are colored. The arrows of ‘homo association and modification’ and ‘homo association and modification with stoichiometric changes’ are revised. The reaction of ‘Set Modified from transition state’ is newly added.

Mentions: The previous version of the CADLIVE network constructor was a software suite for drawing a large-scale map of molecular interactions and for registering their associated regulator-reaction equations (RREs) in an extension of SBML level 2 (7,12). Notice that the previous version neither presents any method for the domain-level drawings nor does implement any pathway analyzer. CADLIVE basically improves Kohn's explicit MIM notation in terms of computer simulation, which describes signal transduction pathways and metabolic circuits in a form that can be readily processed by both computers and humans. Thus, CADLIVE enables compactly drawing complex reactions in the temporal order of reactions, such as multicomplex formation, protein modification, regulation of transcription and transport between organelles. The previous notations for CADLIVE are improved as shown in Figure 1, where some reaction arrows are revised to clearly distinguish their reactions.Figure 1.


Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis.

Kurata H, Inoue K, Maeda K, Masaki K, Shimokawa Y, Zhao Q - Nucleic Acids Res. (2007)

Improved graphical notation for regulators and reactions. The previous version of CADLIVE was improved to make clear the type of reactions. The regulator arrows are colored. The arrows of ‘homo association and modification’ and ‘homo association and modification with stoichiometric changes’ are revised. The reaction of ‘Set Modified from transition state’ is newly added.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2175333&req=5

Figure 1: Improved graphical notation for regulators and reactions. The previous version of CADLIVE was improved to make clear the type of reactions. The regulator arrows are colored. The arrows of ‘homo association and modification’ and ‘homo association and modification with stoichiometric changes’ are revised. The reaction of ‘Set Modified from transition state’ is newly added.
Mentions: The previous version of the CADLIVE network constructor was a software suite for drawing a large-scale map of molecular interactions and for registering their associated regulator-reaction equations (RREs) in an extension of SBML level 2 (7,12). Notice that the previous version neither presents any method for the domain-level drawings nor does implement any pathway analyzer. CADLIVE basically improves Kohn's explicit MIM notation in terms of computer simulation, which describes signal transduction pathways and metabolic circuits in a form that can be readily processed by both computers and humans. Thus, CADLIVE enables compactly drawing complex reactions in the temporal order of reactions, such as multicomplex formation, protein modification, regulation of transcription and transport between organelles. The previous notations for CADLIVE are improved as shown in Figure 1, where some reaction arrows are revised to clearly distinguish their reactions.Figure 1.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, 820-8502, Fukuoka, Japan. kurata@bio.kyutech.ac.jp

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.

Show MeSH