Toward a gold standard for benchmarking gene set enrichment analysis

• Published in: Briefings in bioinformatics Vol. 22; no. 1; pp. 545 - 556
• Main Authors: Geistlinger, Ludwig, Csaba, Gergely, Santarelli, Mara, Ramos, Marcel, Schiffer, Lucas, Turaga, Nitesh, Law, Charity, Davis, Sean, Carey, Vincent, Morgan, Martin, Zimmer, Ralf, Waldron, Levi
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 18.01.2021; Oxford Publishing Limited (England)
• Subjects: Benchmarks; Data analysis; Datasets; DNA microarrays; Enrichment; Gene expression; Gene set enrichment analysis; Phenotypes; Problem Solving Protocol; Ribonucleic acid; RNA; gene expression data; microarray; RNA-seq; pathway analysis; gene set 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 data...