The topology of metabolic or protein-protein interaction networks has
been an extensively studied subject. Our primary interest on the topic is how
the context, such as changing physiological state of the system, affects the
network topology and connectivity within- and between the cellular
functional modules and through this obtain better understating about the
control mechanisms of biological systems. In this study we investigated the
changes in network structure as results of oxidative stress. We collected S.
cerevisiae data on protein-protein interactions (DIP), metabolic pathways
(KEGG), gene regulatory relationships (TRANSFAC) into our bioinformatics
system . We collected available experimental gene expression data from S.
cerevisiae during oxidative stress response at different time points .
The data was integrated into the network context by defining criteria for
evaluating presence or absence of proteins in the integrated network.
Swissprot index of S. cerevisiae proteins  was used to translate ORF
identifiers into the expression dataset to Swissprot protein accession
numbers. We thus reduced the networks and reconstructed condition specific
networks corresponding to each expression data by removing all the proteins
that are absent and their incident links. Structural organization of these
networks was compared by studying topological characteristics. We found that
the degree distribution of most of the networks obtained was different from
the power law. Additionally, we found changes in clustering coefficient, i.e.
local connectivity properties, at two specific time points during the
oxidative stress response. Our results suggest the connectivity of the system
is being modulated as a response to stress or other external stimuli.
|Title of host publication
|International Specialised Symposium on Yeasts ISSY25
|Subtitle of host publication
|Systems Biology of Yeasts - from Models to Applications
|Place of Publication
|VTT Technical Research Centre of Finland
|Published - 2006
|MoE publication type
|International Specialised Symposium on Yeasts, ISSY 25 - Espoo, Finland
Duration: 18 Jun 2006 → 21 Jun 2006
|International Specialised Symposium on Yeasts, ISSY 25
|18/06/06 → 21/06/06