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. 2017 Sep 8;6:e26014. doi: 10.7554/eLife.26014

Figure 4. Analyzing vertebral patterns confers heightened sensitivity in discriminating mutant phenotypes compared to analyzing individual vertebrae.

Figure 4.

Figures A-G show results from Monte Carlo simulations using simulated mutant phenotypes. (A) Power of the global test in discriminating a uniform increase in Tot.TMD (characteristic effect size: d = 4) as a function of sample size and alpha value. The dotted line highlights sample sizes with power >0.8. (B) Sensitivity (fraction of times in which p<0.05 when comparing simulated mutant vs. WT fish) for different test procedures. (C) Specificity (1 - fraction of times in which p<0.05 when comparing WT vs. WT fish) for different test procedures. (D) Power as a function effect size for different test procedures (sample size: n = 3; alpha = 0.05). (E) Closeup of figure (D) for smaller effect sizes. (F) Comparison of sensitivity for different phenotypic features (characteristic effect size: d = 4; sample size: n = 3; alpha = 0.05). (G) Sensitivity for non-uniform phenotypic pattern (linear increase from d = 0 at vert 1 to d = 4 at vert 16; n = 3; alpha = 0.05). Figure H-I show results from Monte Carlo simulations using parameter estimates derived from bmp1a-/- mutants. (H) Sensitivity in discriminating different phenotypic features in bmp1a-/- mutants. T-tests using individual vertebrae were performed on data derived from fish scanned at high resolution. (I) Specificity in discriminating different phenotypic features in bmp1a-/- mutants.

Figure 4—source data 1. Zip file containing phenotypic data (one text file per fish) as well as R code used for analysis.
See legend for Figure 2—source data 1 for a listing of phenotypic measures and their abbreviations.
elife-26014-fig4-data1.zip (164.4KB, zip)
DOI: 10.7554/eLife.26014.011
Figure 4—source data 2. Summary of Royston test results.
For these studies we tested two subsets of 8 vertebrae (Group A: Vert 1, 3, 5, 7, 9, 11, 13, and 15; Group B: and Vert 2, 4, 6, 8, 10, 12, 14, and 16). Cent.Th, Neur.Th, Haem.Th.sd, and Cent.Le were all associated with p<0.05 for one or both groups, and thus these phenotypic features were excluded from Monte Carlo simulations.
elife-26014-fig4-data2.docx (125.6KB, docx)
DOI: 10.7554/eLife.26014.012
Figure 4—source data 3. Summary of sensitivity and specificity for different test procedures.
The top table shows results assuming each phenotypic feature is uniformly elevated in simulated mutants (characteristic effect size: d = 4; sample size: n = 3; alpha = 0.05). The bottom table shows results assuming a non-uniform elevation, with the characteristic effect size linearly increasing from d = 0 at vert 1 to d = 4 at vert 16.
elife-26014-fig4-data3.docx (130.6KB, docx)
DOI: 10.7554/eLife.26014.013