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Table 8 Simulation results.

From: Comparison of lists of genes based on functional profiles

Onto. s n m A and B gene lists Testing procedure Pr{rejectH0} (true H0) Pr{rejectH0} (false H0)
Reference: [25]   
MF 88 69 52 AB = Class-by-class 0.0012 0.3903
      Chi-square 0.0334 1
      New global 0.0469 1
      Additional signif. classes 0.04585 0.697
BP 1602 372 328 AB = Class-by-class 0.002 1
      Chi-square 0.162 1
      New global 0.042 1
      Additional signif. classes 0.042 0
CC 298 305 336 AB = Class-by-class 0.0042 1
      Chi-square 0.0775 1
      New global 0.0389 1
      Additional signif. classes 0.0374 0
References: [27] and [28]   
MF 88 110 99 AB Class-by-class 0.0028 0.0729
   k = 46    Chi-square 0.0341 0.998
      New global 0.0428 0.7281
      Additional signif. classes 0.0409 0.659
BP 1722 858 651 AB Class-by-class 0.003 0.351
   k = 318    Chi-square 0.152 1
      New global 0.056 0.997
      Additional signif. classes 0.055 0.646
CC 394 897 679 AB Class-by-class 0.0076 0.9982
   k = 354    Chi-square 0.0883 1
      New global 0.0625 0.9999
      Additional signif. classes 0.0599 0.0018
  1. Probability of rejecting the null hypothesis of equality of profiles at a nominal 5% significance level in different scenarios associated with real case studies at level 10 in the GO. In the column "testing procedure", "Class-by-class" stands for declaring global differences (i.e. rejecting the null hypothesis of profile equality) if at least one significant class is detected in a class-by-class analysis with correction for testing multiplicity; "Chi-square" stands for the classical chi-square test of homogeneity; "New global" stands for the global test presented in this paper and, finally, "Additional signif. classes" stands for step 3 in the algorithm proposed in the methods section, i.e. proportion of simulation replicates where additional significant classes were detected when a class-by-class analysis was unable of any detection.