title: Importance of collection in gene set enrichment analysis of drug response in cancer cell lines.
abstract: Gene set enrichment analysis (GSEA) associates gene sets and phenotypes, its use is predicated on the choice of a pre-defined collection of sets. The defacto standard implementation of GSEA provides seven collections yet there are no guidelines for the choice of collections and the impact of such choice, if any, is unknown. Here we compare each of the standard gene set collections in the context of a large dataset of drug response in human cancer cell lines. We define and test a new collection based on gene co-expression in cancer cell lines to compare the performance of the standard collections to an externally derived cell line based collection. The results show that GSEA findings vary significantly depending on the collection chosen for analysis. Henceforth, collections should be carefully selected and reported in studies that leverage GSEA.
authors: Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal, University of Montreal, Montreal, Quebec, Canada.
authors: Alain R
authors: AR
authors: Bateman
authors: Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal, University of Montreal, Montreal, Quebec, Canada.
authors: Nehme
authors: N
authors: El-Hachem
authors: Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA.
authors: Andrew H
authors: AH
authors: Beck
authors: 1] Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA [2] Department of Radiation Oncology & Radiology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA [3] Department of Radiation Oncology, Maastricht University, Maastricht, The Netherlands.
authors: Hugo J W L
authors: HJ
authors: Aerts
authors: 1] Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal, University of Montreal, Montreal, Quebec, Canada [2] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
authors: Benjamin
authors: B
authors: Haibe-Kains
mesh_terms: D000465:Algorithms; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D009369:Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D004364:Pharmaceutical Preparations / Q000378:metabolism*
chemical_list: D004364:Pharmaceutical Preparations