title: The Molecular Signatures Database (MSigDB) hallmark gene set collection.
abstract: The Molecular Signatures Database (MSigDB) is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis. Since its creation, MSigDB has grown beyond its roots in metabolic disease and cancer to include >10,000 gene sets. These better represent a wider range of biological processes and diseases, but the utility of the database is reduced by increased redundancy across, and heterogeneity within, gene sets. To address this challenge, here we use a combination of automated approaches and expert curation to develop a collection of "hallmark" gene sets as part of MSigDB. Each hallmark in this collection consists of a "refined" gene set, derived from multiple "founder" sets, that conveys a specific biological state or process and displays coherent expression. The hallmarks effectively summarize most of the relevant information of the original founder sets and, by reducing both variation and redundancy, provide more refined and concise inputs for gene set enrichment analysis.
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA.
authors.forename: Arthur
authors.initials: A
authors.lastname: Liberzon
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA.
authors.forename: Chet
authors.initials: C
authors.lastname: Birger
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA.
authors.forename: Helga
authors.initials: H
authors.lastname: Thorvaldsdóttir
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA.
authors.forename: Mahmoud
authors.initials: M
authors.lastname: Ghandi
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA; Department of Medicine, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92093, USA.
authors.forename: Jill P
authors.initials: JP
authors.lastname: Mesirov
authors.affiliation: Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA; Department of Medicine, UC San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, UC San Diego, La Jolla, CA 92093, USA; Broad Institute of MIT and Harvard, 415 Main St. Cambridge, MA 02142, USA.
authors.forename: Pablo
authors.initials: P
authors.lastname: Tamayo
keywords: gene expression; gene set enrichment analysis; gene sets