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Gaussian Network

Some values of the empirically estimated performance measures for the tests of differential connectivity of single genes are provided in Tables 2 and 3 of the paper. More detailed tables are given below. The targeted nominal level for each of the tables is either 5% or 10%. The number of important genes is 10. The total number of genes is p. Values for the performance of the uncorrected and Benjamini-Hochberg procedures are provided.

Correlation
p=20, &alpha=5% Sensitivity Specificity True Discovery Rate (TDR) True Non-discovery Rate (TNR)
n &rho Power none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg
50 0.5 1 0.99 0.983 0.949 0.97 0.951 0.97 0.989 0.982
200 0.5 1 1 1 0.946 0.97 0.949 0.971 1 1
50 0.6 1 1 0.999 0.946 0.966 0.949 0.967 1 0.999
200 0.6 1 1 1 0.948 0.972 0.95 0.973 1 1
50 0.7 1 1 1 0.948 0.969 0.951 0.97 1 1
200 0.7 1 1 1 0.95 0.973 0.952 0.973 1 1
50 0.8 1 1 1 0.946 0.967 0.949 0.968 1 1
200 0.8 1 1 1 0.946 0.968 0.949 0.969 1 1
50 0.9 1 1 1 0.946 0.969 0.948 0.97 1 1
200 0.9 1 1 1 0.948 0.968 0.95 0.969 1 1


p=20, &alpha=10% Sensitivity Specificity True Discovery Rate (TDR) True Non-discovery Rate (TNR)
n &rho Power none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg
50 0.5 1 0.995 0.99 0.899 0.941 0.908 0.944 0.994 0.989
200 0.5 1 1 1 0.897 0.938 0.907 0.942 1 1
50 0.6 1 1 1 0.897 0.938 0.907 0.942 1 1
200 0.6 1 1 1 0.902 0.942 0.911 0.945 1 1
50 0.7 1 1 1 0.897 0.941 0.906 0.944 1 1
200 0.7 1 1 1 0.903 0.941 0.912 0.945 1 1
50 0.8 1 1 1 0.902 0.939 0.91 0.942 1 1
200 0.8 1 1 1 0.893 0.936 0.903 0.94 1 1
50 0.9 1 1 1 0.9 0.939 0.909 0.943 1 1
200 0.9 1 1 1 0.904 0.941 0.912 0.944 1 1


p=100, &alpha=5% Sensitivity Specificity True Discovery Rate (TDR) True Non-discovery Rate (TNR)
n &rho Power none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg
50 0.5 1 0.76 0.34 0.947 0.996 0.616 0.913 0.973 0.931
200 0.5 1 1 0.999 0.949 0.994 0.687 0.946 1 1
50 0.6 1 0.918 0.621 0.948 0.995 0.664 0.929 0.991 0.959
200 0.6 1 1 1 0.949 0.994 0.686 0.946 1 1
50 0.7 1 0.986 0.862 0.948 0.993 0.676 0.935 0.998 0.985
200 0.7 1 1 1 0.949 0.993 0.685 0.943 1 1
50 0.8 1 0.998 0.964 0.946 0.992 0.674 0.934 1 0.996
200 0.8 1 1 1 0.949 0.994 0.685 0.949 1 1
50 0.9 1 1 0.996 0.946 0.992 0.675 0.936 1 1
200 0.9 1 1 1 0.949 0.994 0.684 0.948 1 1


p=100, &alpha=10% Sensitivity Specificity True Discovery Rate (TDR) True Non-discovery Rate (TNR)
n &rho Power none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg
50 0.5 1 0.853 0.448 0.896 0.992 0.478 0.861 0.982 0.942
200 0.5 1 1 1 0.9 0.987 0.525 0.894 1 1
50 0.6 1 0.962 0.729 0.898 0.989 0.513 0.877 0.995 0.97
200 0.6 1 1 1 0.899 0.987 0.524 0.893 1 1
50 0.7 1 0.995 0.92 0.899 0.987 0.522 0.884 0.999 0.991
200 0.7 1 1 1 0.898 0.987 0.522 0.893 1 1
50 0.8 1 0.999 0.984 0.898 0.985 0.522 0.882 1 0.998
200 0.8 1 1 1 0.898 0.987 0.522 0.896 1 1
50 0.9 1 1 0.998 0.897 0.985 0.519 0.882 1 1
200 0.9 1 1 1 0.899 0.986 0.525 0.892 1 1


Partial Least Squares
p=20, &alpha=5% Sensitivity Specificity True Discovery Rate (TDR) True Non-discovery Rate (TNR)
n &rho Power none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg
50 0.5 0.223 0.113 0.017 0.943 0.994 0.664 0.731 0.515 0.503
200 0.5 0.903 0.354 0.148 0.905 0.97 0.789 0.83 0.583 0.532
50 0.6 0.215 0.108 0.017 0.935 0.992 0.624 0.671 0.512 0.502
200 0.6 0.945 0.464 0.244 0.852 0.935 0.758 0.789 0.614 0.553
50 0.7 0.263 0.134 0.03 0.904 0.983 0.584 0.636 0.511 0.503
200 0.7 0.978 0.583 0.389 0.76 0.862 0.708 0.738 0.646 0.585
50 0.8 0.287 0.157 0.044 0.849 0.959 0.51 0.522 0.502 0.501
200 0.8 0.991 0.73 0.601 0.589 0.684 0.64 0.656 0.686 0.632
50 0.9 0.359 0.177 0.061 0.788 0.936 0.455 0.488 0.489 0.499
200 0.9 0.997 0.883 0.832 0.366 0.421 0.582 0.59 0.758 0.715


p=20, &alpha=10% Sensitivity Specificity True Discovery Rate (TDR) True Non-discovery Rate (TNR)
n &rho Power none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg
50 0.5 0.334 0.186 0.035 0.889 0.984 0.626 0.678 0.522 0.505
200 0.5 0.947 0.48 0.234 0.838 0.935 0.748 0.784 0.617 0.55
50 0.6 0.318 0.184 0.034 0.876 0.983 0.597 0.667 0.518 0.504
200 0.6 0.962 0.594 0.37 0.757 0.874 0.71 0.745 0.651 0.581
50 0.7 0.375 0.215 0.055 0.834 0.963 0.565 0.598 0.515 0.505
200 0.7 0.99 0.704 0.521 0.638 0.768 0.661 0.692 0.683 0.616
50 0.8 0.385 0.246 0.086 0.752 0.923 0.498 0.527 0.499 0.502
200 0.8 0.997 0.827 0.727 0.459 0.554 0.605 0.62 0.726 0.67
50 0.9 0.455 0.265 0.112 0.687 0.876 0.459 0.475 0.483 0.497
200 0.9 0.999 0.928 0.9 0.26 0.299 0.557 0.562 0.784 0.749


p=100, &alpha=5% Sensitivity Specificity True Discovery Rate (TDR) True Non-discovery Rate (TNR)
n &rho Power none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg
50 0.5 0.842 0.084 0.008 0.955 0.996 0.17 0.161 0.904 0.9
200 0.5 0.987 0.134 0.011 0.946 0.997 0.217 0.293 0.908 0.901
50 0.6 0.918 0.089 0.007 0.957 0.996 0.188 0.184 0.904 0.9
200 0.6 0.994 0.12 0.008 0.943 0.997 0.189 0.211 0.906 0.9
50 0.7 0.979 0.092 0.01 0.957 0.995 0.194 0.193 0.905 0.901
200 0.7 0.999 0.106 0.009 0.93 0.995 0.143 0.159 0.903 0.9
50 0.8 1 0.082 0.004 0.965 0.998 0.207 0.235 0.904 0.9
200 0.8 1 0.074 0.005 0.928 0.994 0.102 0.093 0.9 0.9
50 0.9 1 0.08 0.007 0.964 0.997 0.199 0.213 0.904 0.9
200 0.9 1 0.046 0.005 0.911 0.989 0.055 0.053 0.896 0.9


p=100, &alpha=10% Sensitivity Specificity True Discovery Rate (TDR) True Non-discovery Rate (TNR)
n &rho Power none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg
50 0.5 0.898 0.154 0.017 0.907 0.989 0.155 0.146 0.906 0.901
200 0.5 0.998 0.225 0.02 0.895 0.994 0.193 0.275 0.912 0.901
50 0.6 0.951 0.161 0.019 0.914 0.99 0.172 0.174 0.907 0.901
200 0.6 0.997 0.207 0.021 0.889 0.991 0.171 0.198 0.91 0.901
50 0.7 0.992 0.163 0.021 0.915 0.988 0.176 0.165 0.908 0.901
200 0.7 1 0.18 0.02 0.87 0.986 0.133 0.133 0.905 0.9
50 0.8 1 0.152 0.012 0.926 0.995 0.186 0.213 0.908 0.901
200 0.8 1 0.134 0.016 0.865 0.985 0.099 0.104 0.9 0.9
50 0.9 1 0.14 0.012 0.925 0.994 0.171 0.183 0.906 0.901
200 0.9 1 0.09 0.012 0.842 0.977 0.06 0.056 0.893 0.899


Partial Correlation
p=20, &alpha=5% Sensitivity Specificity True Discovery Rate (TDR) True Non-discovery Rate (TNR)
n &rho Power none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg
50 0.5 0.075 0.06 0.007 0.95 0.994 0.543 0.541 0.503 0.5
200 0.5 0.921 0.228 0.037 0.948 0.994 0.813 0.86 0.551 0.508
50 0.6 0.048 0.052 0.004 0.953 0.996 0.527 0.513 0.501 0.5
200 0.6 0.905 0.225 0.036 0.948 0.995 0.812 0.876 0.55 0.508
50 0.7 0.046 0.051 0.004 0.95 0.996 0.504 0.506 0.5 0.5
200 0.7 0.859 0.199 0.028 0.944 0.995 0.781 0.84 0.541 0.506
50 0.8 0.026 0.042 0.003 0.948 0.996 0.447 0.447 0.497 0.5
200 0.8 0.687 0.156 0.018 0.942 0.994 0.729 0.765 0.527 0.503
50 0.9 0.006 0.027 0.002 0.946 0.997 0.336 0.341 0.493 0.5
200 0.9 0.385 0.108 0.008 0.946 0.997 0.668 0.714 0.515 0.501


p=20, &alpha=10% Sensitivity Specificity True Discovery Rate (TDR) True Non-discovery Rate (TNR)
n &rho Power none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg none Benjamini-Hochberg
50 0.5 0.158 0.117 0.013 0.901 0.99 0.54 0.563 0.505 0.501
200 0.5 0.969 0.363 0.078 0.902 0.984 0.787 0.835 0.586 0.516
50 0.6 0.115 0.106 0.008 0.905 0.992 0.526 0.484 0.503 0.5
200 0.6 0.961 0.359 0.076 0.897 0.987 0.777 0.856 0.583 0.517
50 0.7 0.108 0.105 0.008 0.896 0.992 0.501 0.512 0.5 0.5
200 0.7 0.946 0.325 0.063 0.897 0.985 0.759 0.803 0.571 0.512
50 0.8 0.046 0.084 0.007 0.9 0.991 0.457 0.429 0.496 0.499
200 0.8 0.833 0.269 0.04 0.89 0.984 0.71 0.71 0.549 0.506
50 0.9 0.009 0.062 0.005 0.897 0.99 0.376 0.353 0.489 0.499
200 0.9 0.581 0.202 0.019 0.894 0.992 0.656 0.689 0.528 0.503