CADLIVE-Based Analysis for the Budding Yeast Cell Cycle

Abstract

The completion of the yeast genome sequence and the subsequent postgenomic studies regardingtranscriptome and proteome (http://www.yeastgenome.org/, http://mips.gsf.de/proj/yeast/CYGD/db/) remind one how one understands the gene regulatory networks at the molecular level.With the increase in the postgenomic data, the further understanding of the mechanisms of thebudding cell cycle networks requires comprehensive tools for the representation of large-scale signaltransduction pathways, which have been provided by advanced molecular biology, and the integrationof DNA microarray data and protein-protein interaction data into the network. Consequently, thewell-designed map enables one to simulate the molecular process dynamically. In order to ful ll theserequirements, the CADLIVE (Computer-AidedDesign of LIVing systEms)System has beendevelopedthat allows to construct a large-scale map of complicated signal transduction pathways and to simulateit [1].In this paper, the CADLIVE System designs a large-scale map of the budding yeast cell cycle andsearches its signal transduction pathways computationally. The use of CADLIVE enables one to lookat the whole view of the large-scale map, to integrate postgenomic data into the biochemical map. Theinconsistency between the network map and the postgenomic data greatly facilitates predicting novelor unexpected biochemical interactions. Based on the well-designed map, the CADLIVE Simulatorsimulated the budding yeast cell cycle dynamically.