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Table 5 Performance metrics for the assessment of cross-platform transferability of signature genes of k-NN models based on the SEQC NB data

From: An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era

Direction Endpoint Gene set Microarray models Is predict microarray validation samples RNA-Seq models predict RNA-Seq validation samples T-index
Accuracy AUC Accuracy AUC
Mean 95% CI Mean 95% CI Mean 95% CI Mean 95% CI
From microarray to RNA-Seq A* A 0.732 0.667-0.775 0.708 0.645-0.758 0.728 0.653-0.771 0.696 0.627-0.746 0.729
B 0.721 0.655-0.759 0.691 0.631-0.733 0.714 0.647-0.759 0.678 0.614-0.726 0.716
C 0.696 0.639-0.735 0.664 0.609-0.704 0.702 0.654-0.747 0.670 0.631-0.713 0.700
B* A 0.780 0.747-0.811 0.667 0.615-0.72 0.787 0.755-0.815 0.648 0.601-0.694 0.786
B 0.777 0.743-0.807 0.643 0.585-0.704 0.794 0.755-0.827 0.659 0.580-0.725 0.791
C 0.789 0.739-0.827 0.678 0.613-0.732 0.788 0.747-0.819 0.660 0.620-0.711 0.788
C* A 0.978 0.971-0.992 0.978 0.971-0.992 0.992 0.992-0.992 0.992 0.992-0.992 0.992
B 0.989 0.983-0.992 0.989 0.984-0.992 0.989 0.983-0.992 0.989 0.984-0.992 0.989
C 0.931 0.900-0.954 0.935 0.905-0.958 0.988 0.975-0.992 0.988 0.976-0.992 0.984
D* A 0.934 0.882-0.971 0.920 0.863-0.962 0.921 0.882-0956 0.895 0.848-0.940 0.921
B 0.947 0.824-0.978 0.938 0.798-0.973 0.933 0.772-0.978 0.915 0.737-0.967 0.934
C 0.915 0.838-0.956 0.911 0.841-0.961 0.921 0.853-0.963 0.914 0.840-0.956 0.920
E* A 0.624 0.533-0.700 0.534 0.463-0.615 0.606 0.522-0.689 0.537 0.460-0.617 0.612
B 0.562 0.478-0.623 0.507 0.417-0.588 0.569 0.500-0.633 0.519 0.443-0.595 0.566
C 0.607 0.511-0.689 0.513 0.437-0.603 0.599 0.511-0.689 0.515 0.438-0.603 0.602
F* A 0.513 0.444-0.589 0.513 0.446-0.585 0.510 0.433-0.589 0.510 0.426-0.589 0.511
B 0.507 0.456-0.567 0.511 0.452-0.572 0.490 0.422-0.556 0.498 0.431-0.562 0.498
C 0.532 0.456-0.611 0.534 0.460-0.609 0.527 0.444-0.611 0.531 0.448-0.611 0.529
From RNA-Seq to microarray A* A 0.701 0.614-0.759 0.669 0.590-0.732 0.709 0.643-0.759 0.671 0.603-0.727 0.703
B 0.680 0.584-0.741 0.644 0.543-0.708 0.693 0.604-0.747 0.651 0.568-0.710 0.684
C 0.719 0.647-0.767 0.691 0.618-0.748 0.730 0.648-0.771 0.698 0.621-0.743 0.722
B* A 0.775 0.715-0.819 0.662 0.576-0.737 0.775 0.733-0.811 0.640 0.579-0.696 0.775
B 0.777 0.715-0.819 0.639 0.552-0.713 0.785 0.735-0.825 0.640 0.566-0.718 0.778
C 0.792 0.749-0.823 0.681 0.621-0.757 0.790 0.753-0.819 0.659 0.606-0.728 0.791
C* A 0.971 0.967-0.992 0.972 0.969-0.992 0.984 0.983-0.992 0.985 0.984-0.992 0.971
B 0.939 0.900-0.950 0.943 0.901-0.954 0.990 0.988-0.992 0.990 0.988-0.992 0.939
C 0.987 0.975-0.992 0.987 0.975-0.992 0.987 0.971-0.992 0.987 0.972-0.992 0.987
D* A 0.914 0.809-0.971 0.899 0.792-0.957 0.927 0.868-0.963 0.910 0.841-0.951 0.915
B 0.918 0.838-0.963 0.907 0.825-0.962 0.928 0.860-0.971 0.908 0.836-0.957 0.918
C 0.937 0.875-0.978 0.923 0.853-0.973 0.933 0.882-0.971 0.913 0.882-0.962 0.937
E* A 0.598 0.456-0.689 0.506 0.414-0.606 0.598 0.444-0.700 0.522 0.400-0.630 0.598
B 0612 0.511-0.700 0.513 0.432-0.602 0.588 0.489-0.678 0.510 0.415-0.613 0.603
C 0.582 0.478-0.667 0.512 0.412-0.633 0.596 0.500-0.689 0.522 0.432-0.615 0.587
F* A 0.507 0.433-0.600 0.502 0.421-0.590 0.498 0.400-0.600 0.496 0.406-0.597 0.503
B 0.500 0.411-0.595 0.503 0.414-0.596 0.493 0.400-0.589 0.503 0.411-0.601 0.496
C 0.523 0.456-0.600 0.527 0.452-0.602 0.498 0.405-0.578 0.505 0.411-0.59 0.511
  1. A*: A_EFS_All; B*: B_OS_All; C*: C_SEX_All; D*: D_FAV_All; E*: E_EFS_HR; F*: F_OS_HR; AUC: Area under ROC curve; CI: Confidence interval; 95% CI was calculated from the bootstrap estimation. The upper-right and lower-left regions are for the untrained models built using cross-platform transferred signature genes, while the upper-left and lower-right regions are for the models originally trained.
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Genome Biology

ISSN: 1474-760X

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