GPX: Interactive Mining of Gene Expression Data

Discovering co-expressed genes and coherent ex-pression patterns in gene expression data is an important data analysis task in bioinformatics re-search and biomedical applications. Although various clustering methods have been proposed, two tough challenges still remain on how to in-tegrate the users ’ domain knowledge and how to handle the high connectivity in the data. Recently, we have systematically studied the problem and proposed an effective approach [3]. In this paper, we describe a demonstration of GPX (for Gene Pattern eXplorer), an integrated environment for interactive exploration of coherent expression pat-terns and co-expressed genes in gene expression data. GPX integrates several novel techniques, in-cluding the coherent pattern index graph, a gene annotation panel, and a graphical interface, to adopt users ’ domain knowledge and support ex-plorative operations in the clustering procedure. The GPX system as well as its techniques will be showcased, and the progress of GPX will be exemplified using several real-world gene expres-sion data sets.