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Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data

Fig 8

Empirical JTK_CYCLE with asymmetry search of 4 h (eJTK_aby4) identifies more genes than ANOVA, F24, and the other JTK_CYCLE methods.

(A) The vertical axis shows the number of genes with a p-value below or equal to the horizontal axis for the methods indicated. The rightmost point on the horizontal axis is 0.2. (B) The Benjamini-Hochberg correction for testing multiple genes impacts the relative performance of the different methods. The rightmost point on the horizontal axis is 0.2. The colors are the same as in A. (C) The number of genes with Benjamini-Hochberg adjusted p-values below 0.05 (blue) and below 0.20 (red) with the different methods is shown. (D) A comparison of the intersection (below the diagonal) and union (above the diagonal) of genes identified as rhythmic with Benjamini-Hochberg adjusted p-values less than 0.05 for the different methods. JTK: the original JTK_CYCLE method with Bonferroni correction. JTK_BH: the JTK_CYCLE method with Benjamini-Hochberg correction. eJTK: the JTK_CYCLE method with empirical calculation of the p-values. “_aby4” refers to an asymmetry search every 4 h (at 4, 8, 12, 16, and 20 h).

Fig 8

doi: https://doi.org/10.1371/journal.pcbi.1004094.g008