Toward a gold standard for benchmarking gene set enrichment analysis.

Abstract

MOTIVATION: Although gene set enrichment analysis has become an integral part of high-throughput gene expression data analysis, the assessment of enrichment methods remains rudimentary and ad hoc. In the absence of suitable gold standards, evaluations are commonly restricted to selected datasets and biological reasoning on the relevance of resulting enriched gene sets. RESULTS: We develop an extensible framework for reproducible benchmarking of enrichment methods based on defined criteria for applicability, gene set prioritization and detection of relevant processes. This framework incorporates a curated compendium of 75 expression datasets investigating 42 human diseases. The compendium fea..