Limits...
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
Example models of the explicit, heuristic and combinatorial interpretation in CADLIVE. Tyree types of interpretation for the reactions are described in the side table. The number in the parentheses in the tables indicates the product species in the figures. For any RRE, interpretation is stated as, ‘yes’, ‘no’, or ‘maybe’. ‘Yes’ and ‘no’ mean that the reaction occurs and does not, respectively, which depends on the employed interpretation. In the heuristic column, ‘maybe’ means that it is not known whether the products marked by the number are synthesized. Although the notation of CADLIVE has originally been designed as an explicit MIM, it is possible to apply heuristic and combinatorial interpretation to a map of CADLIVE, because the CADLIVE notation is built based on Kohn's MIM. Note that the RREs generated by the CADLIVE editor correspond to the explicit MIM but does not to the heuristic and combinatorial MIMs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2175333&req=5

Figure 8: Example models of the explicit, heuristic and combinatorial interpretation in CADLIVE. Tyree types of interpretation for the reactions are described in the side table. The number in the parentheses in the tables indicates the product species in the figures. For any RRE, interpretation is stated as, ‘yes’, ‘no’, or ‘maybe’. ‘Yes’ and ‘no’ mean that the reaction occurs and does not, respectively, which depends on the employed interpretation. In the heuristic column, ‘maybe’ means that it is not known whether the products marked by the number are synthesized. Although the notation of CADLIVE has originally been designed as an explicit MIM, it is possible to apply heuristic and combinatorial interpretation to a map of CADLIVE, because the CADLIVE notation is built based on Kohn's MIM. Note that the RREs generated by the CADLIVE editor correspond to the explicit MIM but does not to the heuristic and combinatorial MIMs.

Mentions: Second, CADLIVE, which has originally been developed for computer simulation, does not still present the heuristic and combinatorial MIMs, while Kohn's notation allows for them. If CADLIVE draws all possible interactions and molecules provided by heuristic and combinatorial MIMs, it will need much more space, whereby making a map very complicated or confused. We present an idea to avoid this problem. Since the notation of complex formation in CADLIVE is designed based on Kohn's MIMs, it is possible to apply heuristic or combinatorial interpretation to the CADLIVE map, as exemplified by Figure 8. If heuristic or combinatorial interpretation is applied to the CADLIVE map, users can understand the p53 map in the similar manner to Kohn's notation (Figure 6). However, notice that the RREs generated by CADLIVE correspond to the explicit MIM but does not to the heuristic and combinatorial MIMs. The heuristic and combinatorial interpretations cannot be used for computer simulation.Figure 8.


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)

Example models of the explicit, heuristic and combinatorial interpretation in CADLIVE. Tyree types of interpretation for the reactions are described in the side table. The number in the parentheses in the tables indicates the product species in the figures. For any RRE, interpretation is stated as, ‘yes’, ‘no’, or ‘maybe’. ‘Yes’ and ‘no’ mean that the reaction occurs and does not, respectively, which depends on the employed interpretation. In the heuristic column, ‘maybe’ means that it is not known whether the products marked by the number are synthesized. Although the notation of CADLIVE has originally been designed as an explicit MIM, it is possible to apply heuristic and combinatorial interpretation to a map of CADLIVE, because the CADLIVE notation is built based on Kohn's MIM. Note that the RREs generated by the CADLIVE editor correspond to the explicit MIM but does not to the heuristic and combinatorial MIMs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 8: Example models of the explicit, heuristic and combinatorial interpretation in CADLIVE. Tyree types of interpretation for the reactions are described in the side table. The number in the parentheses in the tables indicates the product species in the figures. For any RRE, interpretation is stated as, ‘yes’, ‘no’, or ‘maybe’. ‘Yes’ and ‘no’ mean that the reaction occurs and does not, respectively, which depends on the employed interpretation. In the heuristic column, ‘maybe’ means that it is not known whether the products marked by the number are synthesized. Although the notation of CADLIVE has originally been designed as an explicit MIM, it is possible to apply heuristic and combinatorial interpretation to a map of CADLIVE, because the CADLIVE notation is built based on Kohn's MIM. Note that the RREs generated by the CADLIVE editor correspond to the explicit MIM but does not to the heuristic and combinatorial MIMs.
Mentions: Second, CADLIVE, which has originally been developed for computer simulation, does not still present the heuristic and combinatorial MIMs, while Kohn's notation allows for them. If CADLIVE draws all possible interactions and molecules provided by heuristic and combinatorial MIMs, it will need much more space, whereby making a map very complicated or confused. We present an idea to avoid this problem. Since the notation of complex formation in CADLIVE is designed based on Kohn's MIMs, it is possible to apply heuristic or combinatorial interpretation to the CADLIVE map, as exemplified by Figure 8. If heuristic or combinatorial interpretation is applied to the CADLIVE map, users can understand the p53 map in the similar manner to Kohn's notation (Figure 6). However, notice that the RREs generated by CADLIVE correspond to the explicit MIM but does not to the heuristic and combinatorial MIMs. The heuristic and combinatorial interpretations cannot be used for computer simulation.Figure 8.

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