Investigating the validity of current network analysis on static conglomerate networks by protein network stratification

Background: A molecular network perspective forms the foundation of systems biology. A common practice in analyzing protein-protein interaction (PPI) networks is to perform network analysis on a conglomerate network that is an assembly of all available binary interactions in a given organism from diverse data sources. Recent studies on network dynamics suggested that this approach might have ignored the dynamic nature of context-dependent molecular systems. Results: In this study, we employed a network stratification strategy to investigate the validity of the current network analysis on conglomerate PPI networks. Using the genome-scale tissue- and condition-specific proteomics data in Arabidopsis thaliana, we present here the first systematic investigation into this question. We stratified a conglomerate A. thaliana PPI network into three levels of context-dependent subnetworks. We then focused on three types of most commonly conducted network analyses, i.e., topological, functional ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Minlu Zhang, Long J. Lu
• Keywords: BMCBI 2010, Conglomerate Network, Conglomerate Ppi Network, PPI Networks