Paper Info
Title
The chemical organization of signaling interactions.
Abstract
Motivation: Cellular chemical signaling pathways form complex networks that are beginning to be studied at the level of chemical kinetics and databases of reactions. Chemical reaction details are traditionally represented as lists of reactions and rates. This does not map readily to the block diagram representation familiar to biologists, and obscures the functional organization of signaling networks. This study examines motifs in signaling chemistry and reports common features that may help to formalize such a mapping between pathway block diagrams and the chemistry. The same motifs may facilitate data representation and provide functional abstraction of the chemistry. Results: I classified 74 interactions between 25 signaling pathways in terms of shared chemical motifs. All interactions in this dataset consist of a few communicating molecules from one set of pathways, and a replicating set of reactions and molecules from another. Each unique combination of interacting pathways duplicates the chemical reaction scheme of this replicating set, but involves different rate constants. Signaling pathways can therefore be described in an object-oriented manner as sets of core reactions with well-defined interfaces between pathways. This generalization lends itself to designing simulators and databases for signaling networks.
Year
DOI
Venue
2002
10.1093/bioinformatics/18.6.855
BIOINFORMATICS
Keywords
Field
DocType
chemical reaction,complex network,rate constant,object oriented,chemical kinetics,signaling pathway,data representation
External Data Representation,Molecule,Computer science,Theoretical computer science,Complex network,Bioinformatics
Journal
Volume
Issue
ISSN
18
6
1367-4803
Citations 
PageRank 
References 
6
1.28
2
Authors
1
Name
Order
Citations
PageRank
Upinder S Bhalla133349.60