Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comment
. 2014 Dec;30(12):513-4.
doi: 10.1016/j.tig.2014.10.001.

Pitfalls in the application of gene-set analysis to genetics studies

Adriana Estela Sedeño-Cortés, Paul Pavlidis
Comment

Pitfalls in the application of gene-set analysis to genetics studies

Adriana Estela Sedeño-Cortés et al. Trends Genet. 2014 Dec.

Abstract

Gene-set analysis (GSA) (‘enrichment’) is a popular approach for the interpretation of genome-wide association studies (GWASs). GSA is most commonly applied to the analysis of transcriptomes, but from the outset it has been considered useful for any study that provides rankings or ‘hit lists’ of genes. The recent review by Mooney et al. [1] is a valuable resource for geneticists wishing to apply GSA to the output of GWASs. Here we describe some additional points of practical importance if the methods are to be applied and interpreted soundly.

PubMed Disclaimer

Comment in

Comment on

References

    1. Mooney MA, et al. Functional and genomic context in pathway analysis of GWAS data. Trends Genet TIG. 2014 doi: 10.1016/j.tig.2014.07.004. - DOI - PMC - PubMed
    1. Retraction for Dixson et al., Identification of gene ontologies linked to prefrontal–hippocampal functional coupling in the human brain. Proc Natl Acad Sci. 2014 doi: 10.1073/pnas.1414905111. - DOI - PMC - PubMed
    1. Holden M, et al. GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies. Bioinformatics. 2008;24:2784–2785. - PubMed
    1. Torkamani A, et al. Pathway analysis of seven common diseases assessed by genome-wide association. Genomics. 2008;92:265–272. - PMC - PubMed
    1. Heck A, et al. Converging Genetic and Functional Brain Imaging Evidence Links Neuronal Excitability to Working Memory, Psychiatric Disease, and Brain Activity. Neuron. 2014;81:1203–1213. - PMC - PubMed

LinkOut - more resources