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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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A biochemical map of p53 drawn by the extended CADLIVE. Details of the map are clearly displayed by using the extended CADLIVE GUI editor.
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Figure 6: A biochemical map of p53 drawn by the extended CADLIVE. Details of the map are clearly displayed by using the extended CADLIVE GUI editor.

Mentions: To compare the notation of CADLIVE with Kohn's MIMs, we drew the same p53 map as he presented elsewhere(16). As shown in Figure 6, the new notations of the Domain expansion, Virtual reactions and nodes and InnerLink enabled drawing the domain level functions of p53 that are changed by a variety of phosphorylation sites. However, there are two major inconsistencies between CADLIVE and Kohn's notations. One is that CADLIVE definitely needs specifying the temporal order to place a complex species, while the MIMs do not. The other is that CADLIVE allows for the explicit model but does not allow for heuristic and combinatorial interpretation.Figure 6.


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)

A biochemical map of p53 drawn by the extended CADLIVE. Details of the map are clearly displayed by using the extended CADLIVE GUI editor.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 6: A biochemical map of p53 drawn by the extended CADLIVE. Details of the map are clearly displayed by using the extended CADLIVE GUI editor.
Mentions: To compare the notation of CADLIVE with Kohn's MIMs, we drew the same p53 map as he presented elsewhere(16). As shown in Figure 6, the new notations of the Domain expansion, Virtual reactions and nodes and InnerLink enabled drawing the domain level functions of p53 that are changed by a variety of phosphorylation sites. However, there are two major inconsistencies between CADLIVE and Kohn's notations. One is that CADLIVE definitely needs specifying the temporal order to place a complex species, while the MIMs do not. The other is that CADLIVE allows for the explicit model but does not allow for heuristic and combinatorial interpretation.Figure 6.

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