Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium

Biological systems are orchestrated by heterogeneous regulatory programs that control complex processes and adapt to a dynamic environment. Recent advances in high-throughput experimental methods provide genome-wide perspectives on such regulatory programs. A considerable amount of data on the behavior of model systems in a variety of conditions is rapidly accumulating. Still, the dominant paradigm is to analyze new genome-wide experiments separately from any other extant data, for example, by clustering the new data alone. Here we introduce a new methodology for analyzing the results of a new functional genomic study vis-à-vis a large compendium of previously published results from heterogeneous experimental techniques. We demonstrate our methodology on Saccharomyces cerevisiae, using a compendium of some 2000 experiments from 60 different publications. Most importantly, we show how the integrated analysis reveals unexpected connections among biological processes, and differentiates between novel and known effects in the analyzed experiments. Such characterization is impossible when new data sets are studied in isolation. Our results exemplify the power of the integrative approach in the analysis of genomic scale data sets and call for a paradigm shift in their study.