DNA microarrays can be used to identify gene expression changes characteristic of human disease. This is challenging, however, when relevant differences are subtle at the level of individual genes. We introduce an analytical strategy, Gene Set Enrichment Analysis, designed to detect modest but coordinate changes in the expression of groups of functionally related genes. Using this approach, we identify a set of genes involved in oxidative phosphorylation whose expression is coordinately decreased in human diabetic muscle. Expression of these genes is high at sites of insulin-mediated glucose disposal, activated by PGC-1α and correlated with total-body aerobic capacity. Our results associate this gene set with clinically important variation in human metabolism and illustrate the value of pathway relationships in the analysis of genomic profiling experiments.
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We thank C. Ladd, M. Gaasenbeek and G. Ahlqvist for technical assistance; L. Gaffney for preparing illustrations; D. Stram and R. Heinrich for discussions; M. Patti and colleagues for sharing their manuscript before publication; B. Gewurz, E. Rosen, members of D.A. and E.S.L.'s labs for comments on the manuscript; and the individuals who volunteered for this study. V.K.M. is supported by a Howard Hughes Medical Institute physician postdoctoral fellowship. C.M.L. was supported by the Foundation for Strategic Research, the Royal Physiographic Society, the Sven Lundgrens Foundation and the Albert Pahlssons Foundation. T.R.G. is an Investigator of the Howard Hughes Medical Institute. J.N.H. is the recipient of a Career Development Award of the Burroughs Welcome Fund. D.A. is a Clinical Scholar in Translational Research of the Burroughs Welcome Fund and a Charles E. Culpeper Scholar of the Rockefeller Brothers Fund. This work was supported in part by grants from Affymetrix, Millennium Pharmaceuticals and Bristol-Myers Squibb to E.S.L. and from the Sigrid Juselius Foundation, the Juvenile Diabetes Foundation-Wallenberg Foundation, the Swedish Medical Research Council, the Novo-Nordisk Foundation and a European Community Genomics Integrated Force for Type 2 Diabetes grant to L.C.G.
The authors declare no competing financial interests.
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Mootha, V., Lindgren, C., Eriksson, KF. et al. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34, 267–273 (2003). https://doi.org/10.1038/ng1180
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