An Algorithm for Modularization of MAPK and Calcium Signaling Pathways: Comparative Analysis Among Different Species

J Biomed Inform. 2007 Dec;40(6):726-49. doi: 10.1016/j.jbi.2007.05.007. Epub 2007 May 18.

Abstract

Signaling pathways are large complex biochemical networks. It is difficult to analyze the underlying mechanism of such networks as a whole. In the present article, we have proposed an algorithm for modularization of signal transduction pathways. Unlike studying a signaling pathway as a whole, this enables one to study the individual modules (less complex smaller units) easily and hence to study the entire pathway better. A comparative study of modules belonging to different species (for the same signaling pathway) has been made, which gives an overall idea about development of the signaling pathways over the taken set of species of calcium and MAPK signaling pathways. The superior performance, in terms of biological significance, of the proposed algorithm over an existing community finding algorithm of Newman [Newman MEJ. Modularity and community structure in networks. Proc Natl Acad Sci USA 2006;103(23):8577-82] has been demonstrated using the aforesaid pathways of H. sapiens.

Publication types

  • Comparative Study

MeSH terms

  • Algorithms*
  • Animals
  • Artificial Intelligence*
  • Calcium Signaling / physiology*
  • Computer Simulation
  • Humans
  • MAP Kinase Signaling System / physiology*
  • Models, Biological*
  • Species Specificity