An interactive approach to mining gene expression data

Abstract

Effective identification of coexpressed genes and coherent patterns in gene expression data is an important task in bioinformatics research and biomedical applications. Several clustering methods have recently been proposed to identify coexpressed genes that share similar coherent patterns. However, there is no objective standard for groups of coexpressed genes. The interpretation of co-expression heavily depends on domain knowledge. Furthermore, groups of coexpressed genes in gene expression data are often highly connected through a large number of "intermediate" genes. There may be no clear boundaries to separate clusters. Clustering gene expression data also faces the challenges of satisfying biological domain requirements and addressing the high connectivity of the data sets. In this paper, we propose an interactive framework for exploring coherent patterns in gene expression data. A novel coherent pattern index is proposed to give users highly confident indications of the existence of coherent patterns. To derive a coherent pattern index and facilitate clustering, we devise an attraction tree structure that summarizes the coherence information among genes in the data set. We present efficient and scalable algorithms for constructing attraction trees and coherent pattern indices from gene expression data sets. Our experimental results show that our approach is effective in mining gene expression data and is scalable for mining large data sets.