Connectivity, Module-Conformity, and Significance: Understanding Gene Coexpression Network Methods

• Activity Number: 62
• Type: Contributed
• Date/Time: Sunday, August 6, 2006 : 4:00 PM to 5:50 PM
• Sponsor: Biometrics Section
• Author(s): Jun Dong*+ and Steve Horvath and Andy Yip
• Companies: University of California, Los Angeles and University of California, Los Angeles and National University of Singapore
• Keywords: connectivity ; hub gene ; gene network ; clustering coefficient ; module ; module eigengene

Abstract

In gene networks, modules may correspond to pathways. Within modules, highly connected `hub'- nodes have often been found to be biologically or clinically interesting targets. This paper presents theoretical and empirical results that show how intramodular connectivity, the clustering coefficient and other fundamental network concepts are related to each other. We define the concept of node conformity for general networks and use it to relate node-specific and module-specific network concepts to each other. We arrive at the notion of a module eigengene, which effectively summarizes the gene expression profiles of the entire module. We explain the meaning of fundamental network concepts inside a module in terms of the corresponding module eigengene. We provide a simple model for explaining why intramodular hub genes have often been found to be biologically significant.