GPX: Interactive Mining of Gene Expression Data

Abstract

Discovering co-expressed genes and coherent expression patterns in gene expression data is an important data analysis task in bioinformatics research and biomedical applications. Although various clustering methods have been proposed, two tough challenges still remain on how to integrate the users' domain knowledge and how to handle the high connectivity in the data. This chapter proposes an effective approach to analyze the gene expression data. It presents a demonstration of GPX (Gene Pattern eXplorer)—an integrated environment for interactive exploration of coherent expression patterns and co-expressed genes in gene expression data. GPX integrates several novel techniques, including the coherent pattern index graph, a gene annotation panel, and a graphical interface, to adopt users' domain knowledge and support explorative operations in the clustering procedure. The chapter exemplifies the progress of GPX using several real-world gene expression data sets.