Figure 6.

Evaluation of permutation test for DANGER analysis and comparison between dTPM and dDE. (A) Comparison of false detection rates among approximate dTPM (up to 11-MM NRR PAM, t = 0.4, L = 5E-1), optimized dTPM (up to 8-MM NGG PAM, t = 0.4, L = 1E-15), and optimized dDE (up to 8-MM NGG PAM, α = 0.001, L = 1E-15) in GO categories. BP, CC, and MF indicate GO categories of Biological Process, Cellular Component, and Molecular Function, respectively. Error bars represent SEM; asterisk indicates the statistical significance of two-sided Welch’s t-test; cross indicates statistical power (1-ß)>0.8. Mean±SD of n = 10 permutation data set. (B) Comparison of amount of GO terms of all D-index, significant D-index, and expected true D-index among approximate dTPM (up to 11-MM NRR PAM, t = 0.4, L = 5E-1), optimized dTPM (up to 8-MM NGG PAM, t = 0.4, L = 1E-15), and optimized dDE (up to 8-MM NGG PAM, α = 0.001, L = 1E-15), respectively. (C) Comparison of D-index and significant D-index between optimized dTPM and optimized dDE. A Venn diagram comparing the counts of D-index and significant D-index between optimized dTPM and optimized dDE. (D) The list of the top 16 significant D-indices in the optimized dTPM. The D-index values are indicated by bar graphs adjacent to the GO terms.