A Closer Look at “Social” Boundary Genes Reveals Knowledge to Gene Expression Profiles

Shang      Gao; Jia      Zeng; Abdallah      M. ElSheikh; Ghada      Naji; Reda      Alhajj; Jon      Rokne; Douglas      Demetrick

doi:10.2174/1389203711109070602

Abstract

As social network analysis is gaining popularity in modeling real world problems, the task of applying the social network model concepts and notions to biological data is still one of the most attractive research problems to be addressed. According, our work described in this paper focuses on a particular set of genes that reside on the community boundaries in gene co-expression networks. Stemmed from community mining problem in social networks, peripheries of communities (i.e., boundaries) can be used to aid certain biological analysis. The proposed method consists of three parts: 1) Finding communities of gene co-expression networks through clustering. 2) Analyzing stability of community structures by Monte Carlo method. 3) Designing of dynamic adoption of boundaries using geometric convexity. We validated our findings using breast cancer gene expression data from various studies. Our approach contributes to the new branch of applying social network mechanisms in biological data analysis, leading to new data mining strategies implied by witnessing social behaviors in gene expression analysis.

Keywords: Co-expression modules, gene expression profiling, social network mining and analysis, social community, social behavior, Centola, multi-dimensional spaces, convex hulls, silhouette value, Estrogen receptors