Importance of collection in gene set enrichment analysis of drug response in cancer cell lines

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Importance of collection in gene set enrichment analysis of drug response in cancer cell lines

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Title: Importance of collection in gene set enrichment analysis of drug response in cancer cell lines
Author: Bateman, Alain R.; El-Hachem, Nehme; Beck, Andrew H.; Aerts, Hugo J. W. L.; Haibe-Kains, Benjamin

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Citation: Bateman, Alain R., Nehme El-Hachem, Andrew H. Beck, Hugo J. W. L. Aerts, and Benjamin Haibe-Kains. 2014. “Importance of collection in gene set enrichment analysis of drug response in cancer cell lines.” Scientific Reports 4 (1): 4092. doi:10.1038/srep04092. http://dx.doi.org/10.1038/srep04092.
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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.
Published Version: doi:10.1038/srep04092
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923229/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:11879858
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