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A comprehensive modular map of molecular interactions in RB/E2F pathway.

Calzone L, Gelay A, Zinovyev A, Radvanyi F, Barillot E - Mol. Syst. Biol. (2008)

Bottom Line: The network contains more details about RB/E2F interaction network than existing large-scale pathway databases.Structural analysis of the interaction network revealed a modular organization of the network, which was used to elaborate a more summarized, higher-level representation of RB/E2F network.The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway.

View Article: PubMed Central - PubMed

Affiliation: Institut Curie, Service Blolnforrnatique, Paris, France.

ABSTRACT
We present, here, a detailed and curated map of molecular interactions taking place in the regulation of the cell cycle by the retinoblastoma protein (RB/RB1). Deregulations and/or mutations in this pathway are observed in most human cancers. The map was created using Systems Biology Graphical Notation language with the help of CellDesigner 3.5 software and converted into BioPAX 2.0 pathway description format. In the current state the map contains 78 proteins, 176 genes, 99 protein complexes, 208 distinct chemical species and 165 chemical reactions. Overall, the map recapitulates biological facts from approximately 350 publications annotated in the diagram. The network contains more details about RB/E2F interaction network than existing large-scale pathway databases. Structural analysis of the interaction network revealed a modular organization of the network, which was used to elaborate a more summarized, higher-level representation of RB/E2F network. The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway.

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Related in: MedlinePlus

Examples of textual representation of species structure. In CellDesigner, information about sites of phosphorylation or acetylation, and so on can be showed on the protein itself. A complex is represented as a black box surrounding the proteins composing the complex.
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f5: Examples of textual representation of species structure. In CellDesigner, information about sites of phosphorylation or acetylation, and so on can be showed on the protein itself. A complex is represented as a black box surrounding the proteins composing the complex.

Mentions: Here, ‘:' delimitates components of a complex if the species has several components. Optional suffixes ‘active' or ‘hm' describe active state of the chemical species or N-homodimer state. Several examples of such conversion are presented in Figure 5.


A comprehensive modular map of molecular interactions in RB/E2F pathway.

Calzone L, Gelay A, Zinovyev A, Radvanyi F, Barillot E - Mol. Syst. Biol. (2008)

Examples of textual representation of species structure. In CellDesigner, information about sites of phosphorylation or acetylation, and so on can be showed on the protein itself. A complex is represented as a black box surrounding the proteins composing the complex.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2290939&req=5

f5: Examples of textual representation of species structure. In CellDesigner, information about sites of phosphorylation or acetylation, and so on can be showed on the protein itself. A complex is represented as a black box surrounding the proteins composing the complex.
Mentions: Here, ‘:' delimitates components of a complex if the species has several components. Optional suffixes ‘active' or ‘hm' describe active state of the chemical species or N-homodimer state. Several examples of such conversion are presented in Figure 5.

Bottom Line: The network contains more details about RB/E2F interaction network than existing large-scale pathway databases.Structural analysis of the interaction network revealed a modular organization of the network, which was used to elaborate a more summarized, higher-level representation of RB/E2F network.The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway.

View Article: PubMed Central - PubMed

Affiliation: Institut Curie, Service Blolnforrnatique, Paris, France.

ABSTRACT
We present, here, a detailed and curated map of molecular interactions taking place in the regulation of the cell cycle by the retinoblastoma protein (RB/RB1). Deregulations and/or mutations in this pathway are observed in most human cancers. The map was created using Systems Biology Graphical Notation language with the help of CellDesigner 3.5 software and converted into BioPAX 2.0 pathway description format. In the current state the map contains 78 proteins, 176 genes, 99 protein complexes, 208 distinct chemical species and 165 chemical reactions. Overall, the map recapitulates biological facts from approximately 350 publications annotated in the diagram. The network contains more details about RB/E2F interaction network than existing large-scale pathway databases. Structural analysis of the interaction network revealed a modular organization of the network, which was used to elaborate a more summarized, higher-level representation of RB/E2F network. The simplification of complex networks opens the road for creating realistic computational models of this regulatory pathway.

Show MeSH
Related in: MedlinePlus