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Table 2 Prediction accuracy of competitive RNA-RNA binding sites prediction methods.

From: Fast prediction of RNA-RNA interaction

  Sensitivity PPV F-measure
RNA-RNA interaction pairs inRNAs IntaRNA RNAup inRNAs IntaRNA RNAup inRNAs IntaRNA RNAup
CopA-CopT 0.889 1.000 0.556 0.828 0.391 0.652 0.857 0.562 0.600
DIS-DIS 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
IncRNA54-RepZ 1.000 0.738 0.750 0.889 0.850 0.857 0.941 0.790 0.800
R1inv-R2inv 1.000 1.000 1.000 0.778 1.000 0.778 0.875 1.000 0.875
Tar-Tar* 1.000 1.000 1.000 0.833 0.833 0.833 0.909 0.909 0.909
DsrA-RpoS 0.808 0.808 0.808 0.778 0.778 0.778 0.793 0.793 0.793
GcvB-argT 0.950 0.950 0.900 0.864 0.950 0.947 0.905 0.950 0.923
GcvB-dppA 1.000 1.000 1.000 0.850 0.586 0.459 0.919 0.739 0.629
GcvB-gltI 0.750 0.000 0.000 0.500 0.000 0.000 0.600 0.000 0.000
GcvB-livJ 0.634 0.955 0.955 0.824 0.955 0.955 0.717 0.955 0.955
GcvB-livK 0.540 0.542 0.542 0.570 0.565 0.565 0.555 0.553 0.553
GcvB-oppA 1.000 1.000 1.000 0.733 0.957 0.957 0.846 0.978 0.978
GcvB-STM4351 0.760 0.760 0.880 1.000 0.905 0.957 0.864 0.826 0.917
IstR-tisAB 0.722 0.879 0.667 1.000 0.960 1.000 0.839 0.918 0.800
MicA-ompA 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000 1.000
MicA-lamB 1.000 1.000 0.826 1.000 0.821 0.704 1.000 0.902 0.760
MicC-ompC 1.000 1.000 0.727 1.000 0.537 0.410 1.000 0.699 0.524
MicF-ompF 0.960 0.960 0.800 0.960 0.960 0.952 0.960 0.960 0.869
OxyS-fhlA 0.813 0.500 0.375 1.000 1.000 1.000 0.897 0.667 0.545
RyhB-sdhD 0.618 0.588 0.794 0.955 1.000 0.794 0.750 0.741 0.794
RyhB-sodB 1.000 1.000 1.000 1.000 0.818 0.900 1.000 0.900 0.947
SgrS-ptsG 0.566 0.739 0.739 0.765 1.000 1.000 0.651 0.850 0.850
Spot42-galK 0.432 0.409 0.523 0.760 0.643 0.523 0.551 0.500 0.523
Average 0.845 0.819 0.776 0.865 0.805 0.784 0.845 0.791 0.763
  1. This Table shows the sensitivity, PPV and F-measure for RNA-RNA binding sites prediction by (1) inRNAs, (2) IntaRNA[16], and (3) RNAup [15]. The dataset is compiled by Kato et al. [13] and Busch et al. [16].