Skip to main content

Table 7 Performance metrics for the assessment of cross-platform transferability of signature genes of predictive models based on the TCGA AML data

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

Algorithm Direction Endpoint Gene set Microarray model RNA-Seqmodel T-index
Accuracy AUC Accuracy AUC
Mean 95% CI Mean 95% CI Mean 95% CI Mean 95% CI
k-NN Forward Sex A 0.988 0.988-0.988 0.987 0.987-0.987 0.988 0.988-0.988 0.987 0.987-0.987 0.988
B 0.980 0.953-0.988 0.980 0.955-0.987 0.986 0.977-0.988 0.985 0.977-0.987 0.986
C 0.496 0.419-0.57 0.496 0.413-0.579 0.734 0.419-0.988 0.733 0.418-0.987 0.647
Cyto Risk A 0.945 0.907-0.988 0.895 0.805-0.993 0.947 0.872-0.988 0.905 0.794-0.993 0.947
B 0.939 0.872-0.977 0.904 0.745-0.986 0.942 0.884-0.977 0.925 0.825-0.986 0.942
C 0.919 0.848-0.965 0.884 0.767-0.964 0.907 0.872-0.953 0.854 0.776-0.948 0.908
Reverse Sex A 0.988 0.988-0.988 0.987 0.987-0.987 0.988 0.988-0.988 0.987 0.987-0.987 0.988
B 0.508 0.419-0.599 0.501 0.41-0.591 0.506 0.407-0.593 0.508 0.409-0.593 0.507
C 0.977 0.977-0.977 0.977 0.977-0.977 0.988 0.988-0.988 0.987 0.987-0.987 0.977
Cyto Risk A 0.937 0.837-0.988 0.886 0.724-0.993 0.951 0.843-0.988 0.924 0.815-0.993 0.938
B 0.856 0.744-0.919 0.758 0.59-0.888 0.848 0.767-0.907 0.748 0.589-0.893 0.855
C 0.930 0.86-0.965 0.887 0.767-0.979 0.943 0.86-0.988 0.920 0.746-0.993 0.930
NSC Forward Sex A 0.988 0.988-0.988 0.987 0.987-0.987 0.988 0.988-0.988 0.987 0.987-0.987 0.988
B 0.983 0.977-0.988 0.982 0.977-0.987 0.988 0.988-0.988 0.987 0.987-0.987 0.988
C 0.471 0.419-0.547 0.454 0.398-0.531 0.725 0.488-0.988 0.701 0.46-0.987 0.619
Cyto Risk A 0.937 0.907-0.953 0.857 0.75-0.907 0.951 0.919-0.977 0.904 0.836-0.979 0.950
B 0.892 0.837-0.93 0.860 0.707-0.933 0.891 0.872-0.907 0.873 0.801-0.919 0.891
C 0.889 0.849-0.907 0.812 0.666-0.871 0.876 0.86-0.919 0.775 0.625-0.829 0.877
Reverse Sex A 0.988 0.988-0.988 0.987 0.987-0.987 0.988 0.988-0.988 0.987 0.987-0.987 0.988
B 0.526 0.453-0.547 0.487 0.439-0.52 0.504 0.436-0.547 0.481 0.426-0.52 0.515
C 0.988 0.988-0.988 0.987 0.987-0.987 0.988 0.988-0.988 0.987 0.987-0.987 0.988
Cyto Risk A 0.926 0.872-0.977 0.828 0.656-0.986 0.929 0.907-0.977 0.913 0.846-0.986 0.927
B 0.854 0.814-0.895 0.609 0.5-0.743 0.820 0.814-0.837 0.521 0.5-0.562 0.849
C 0.907 0.884-0.925 0.907 0.863-0.954 0.886 0.872-0.942 0.852 0.794-0.964 0.905
SVM Forward Sex A 0.980 0.965-0.988 0.980 0.966-0.987 0.988 0.988-0.988 0.987 0.987-0.987 0.988
B 0.981 0.942-0.988 0.981 0.945-0.987 0.984 0.977-0.988 0.983 0.974-0.987 0.984
C 0.516 0.43-0.593 0.515 0.429-0.599 0.753 0.43-0.988 0.752 0.426-0.987 0.671
Cyto Risk A 0.939 0.895-0.988 0.879 0.774-0.993 0.957 0.895-0.988 0.919 0.774-0.993 0.956
B 0.963 0.919-0.988 0.941 0.829-0.993 0.961 0.93-0.988 0.947 0.868-0.993 0.961
C 0.919 0.884-0.953 0.901 0.832-0.964 0.920 0.86-0.965 0.888 0.736-0.979 0.920
Reverse Sex A 0.981 0.965-0.988 0.980 0.964-0.987 0.988 0.988-0.988 0.987 0.987-0.987 0.981
B 0.493 0.407-0.593 0.489 0.404-0.592 0.497 0.407-0.593 0.497 0.409-0.588 0.495
C 0.982 0.977-0.988 0.982 0.977-0.987 0.988 0.977-0.988 0.987 0.974-0.987 0.983
Cyto Risk A 0.932 0.872-0.977 0.871 0.739-0.962 0.965 0.919-0.988 0.955 0.812-0.993 0.932
B 0.845 0.756-0.919 0.778 0.608-0.895 0.869 0.779-0.942 0.787 0.583-0.925 0.847
C 0.944 0.872-0.977 0.901 0.729-962 0.964 0.907-0.988 0.944 0.846-0.993 0.944
  1. AUC: Area under ROC curve; CI: Confidence interval; 95% CI was calculated from the bootstrap estimation.
  2. 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 cross-platform prediction of the models (the training and validation samples were profiled with different platforms), while the upper-left and lower-right regions are for the intra-platform prediction of the models (both training and validation samples were profiled with the same platform).