Curbing false discovery rates in interpretation of genome-wide expression profiles.
Fisher's exact test is widely used in biomedical research, particularly in genomic profile analysis. Since in most databases, the frequency distribution of genes is right skewed, we show here that its use can lead to excessive false-positive discoveries. We propose to apply Zelen's exact test on a stratification of the gene set; this solves the false discovery problem, and should avoid misleading interpretations of lists of genes produced by various genome-wide analysis technologies.
Université Joseph Fourier, Grenoble, France; Laboratoire Jean Kuntzmann, CNRS UMR 5224, Grenoble, France; Laboratoire d'Excellence 'TOUCAN', Toulouse, France. Electronic address: Bernard.Ycart@imag.fr.
Bernard
B
Ycart
Laboratoire d'Excellence 'TOUCAN', Toulouse, France; INSERM UMR1037, Cancer Research Center of Toulouse, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France; ERL 5294 CNRS, Toulouse, France.
Frédéric
F
Pont
Laboratoire d'Excellence 'TOUCAN', Toulouse, France; INSERM UMR1037, Cancer Research Center of Toulouse, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France; ERL 5294 CNRS, Toulouse, France.
Jean-Jacques
JJ
Fournié
D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D016208:Databases, Factual; D005189:False Positive Reactions; D020869:Gene Expression Profiling; D055106:Genome-Wide Association Study; D023281:Genomics; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D040901:Proteomics / Q000379:methods; D012107:Research Design; D014158:Transcription, Genetic; D059467:Transcriptome
Genomics; Statistics; Transcriptomics