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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.

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New notations for drawing modular architectures or unknown modules.
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Figure 4: New notations for drawing modular architectures or unknown modules.

Mentions: CADLIVE is able to draw a wide resolution map from the domain level to a phenomenological event level on the ‘Network Constructor’ window. Since complicated drawings often make a network map complicated or confused, we present ‘WhiteBox’ that packs related nodes into a module or a subnetwork as shown in Figure 4. Since WhiteBox is able to include itself, biochemical networks can be drawn in a hierarchical modular architecture. WhiteBox is handled on the menu of ‘List of WhiteBox’. ‘BlackBox’ denotes the subnetwork whose molecular mechanisms or reactions are unknown. It is allowed to place an unknown subnetwork as a BlackBox symbol. BlackBox is edited in the same manner as the species.Figure 4.


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)

New notations for drawing modular architectures or unknown modules.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: New notations for drawing modular architectures or unknown modules.
Mentions: CADLIVE is able to draw a wide resolution map from the domain level to a phenomenological event level on the ‘Network Constructor’ window. Since complicated drawings often make a network map complicated or confused, we present ‘WhiteBox’ that packs related nodes into a module or a subnetwork as shown in Figure 4. Since WhiteBox is able to include itself, biochemical networks can be drawn in a hierarchical modular architecture. WhiteBox is handled on the menu of ‘List of WhiteBox’. ‘BlackBox’ denotes the subnetwork whose molecular mechanisms or reactions are unknown. It is allowed to place an unknown subnetwork as a BlackBox symbol. BlackBox is edited in the same manner as the species.Figure 4.

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