Integrative Approaches for Microarray Data Analysis

Microarrays were one of the first technologies of the genomic revolution to gain widespread adoption, rapidly expanding from a cottage industry to the source of thousands of experimental results. They were one of the first assays for which data repositories and metadata were standardized and researchers were required by many journals to make published data publicly available. Microarrays provide high-throughput insights into the biological functions of genes and gene products; however, they also present a “curse of dimensionality,” whereby the availability of many gene expression measurements in few samples make it challenging to distinguish noise from true biological signal. All of these factors argue for integrative approaches to microarray data analysis, which combine data from multiple experiments to increase sample size, avoid laboratory-specific bias, and enable new biological insights not possible from a single experiment. Here, we discuss several approaches to integrative microarray analysis for a diverse range of applications, including biomarker discovery, gene function and interaction prediction, and regulatory network inference. We also show how, by integrating large microarray compendia with diverse genomic data types, more nuanced biological hypotheses can be explored computationally. This chapter provides overviews and brief descriptions of each of these approaches to microarray integration.