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. 2012 Feb 14;40(9):e70. doi: 10.1093/nar/gks048

Table 7.

Comparison of default and benchmarked performances in histone modification datasets

Dataset Algorithm Default AUCROC Max. AUCROC param. H3.K27 GM-VDA H3.K36 GM-VDA H3.K27 GM H3.K27MT ES.H3K4 ES.H3K2
MYO.H3k27me3.GM.VDA CCAT 0.8232 0.8787 0.0000 −0.1938 −0.0927 −0.1539 −0.1670 −0.2618
MYO.H3k36me3.GM.VDA CCAT 0.6223 0.6849 0.1938 0.0000 0.1011 0.0400 0.0268 −0.0679
MYO.H3k27me3.GM CCAT 0.8002 0.8562 −0.2023 −0.1768 0.0000 −0.0371 −0.1646 −0.2083
MYO.H3k27me3.MT CCAT 0.7355 0.8191 −0.1651 −0.1397 0.0371 0.0000 −0.1274 −0.1712
ES.H3K4me3 CCAT 0.8413 0.8413 −0.0181 −0.2190 −0.0411 −0.1058 0.0000 −0.3386
ES.H3K27me3 CCAT 0.5027 0.6556 −0.0405 −0.0124 0.1431 0.0599 0.1595 0.0000
MYO.H3k27me3.GM.VDA ChipDiff 0.8331 0.8331 0.0000 −0.1635 −0.0452 −0.0991 0.0095 0.0841
MYO.H3k36me3.GM.VDA ChipDiff 0.6696 0.6696 0.1635 0.0000 0.1184 0.0644 0.1731 0.2476
MYO.H3k27me3.GM ChipDiff 0.7879 0.7879 0.0452 −0.1184 0.0000 −0.0539 0.0547 0.1293
MYO.H3k27me3.MT ChipDiff 0.7340 0.7340 0.0991 −0.0644 0.0539 0.0000 0.1087 0.1832
ES.H3K4me3 ChipDiff 0.8426 0.9720 −0.2687 −0.4425 −0.2038 −0.2418 0.0000 −0.1001
ES.H3K27me3 ChipDiff 0.9172 0.9172 −0.0841 −0.2476 −0.1293 −0.1832 −0.0745 0.0000
MYO.H3k27me3.GM.VDA Erange 0.5038 0.5671 0.0000 −0.0672 −0.0011 −0.0587 0.1681 −0.0473
MYO.H3k36me3.GM.VDA Erange 0.5000 0.6110 −0.1221 0.0000 −0.0921 −0.0554 0.1158 −0.0243
MYO.H3k27me3.GM Erange 0.5003 0.5712 −0.0188 −0.0715 0.0000 −0.0559 0.3057 0.2937
MYO.H3k27me3.MT Erange 0.5000 0.5557 −0.0667 0.0554 −0.0367 0.0000 0.1712 0.0311
ES.H3K4me3 Erange 0.8088 0.8770 −0.3245 −0.3772 −0.3057 −0.3617 0.0000 −0.0121
ES.H3K27me3 Erange 0.5826 0.8649 −0.3125 −0.3652 −0.2937 −0.3496 0.0120 0.0000
MYO.H3k27me3.GM.VDA Findpeaks 0.8427 0.8469 0.0000 −0.3916 −0.0482 −0.1119 0.0283 0.1531
MYO.H3k36me3.GM.VDA Findpeaks 0.4610 0.7576 0.0141 0.0000 0.0415 −0.0475 0.0654 0.2424
MYO.H3k27me3.GM Findpeaks 0.7987 0.7991 −0.0274 −0.0415 0.0000 −0.0889 0.0239 0.2009
MYO.H3k27me3.MT Findpeaks 0.7350 0.8423 −0.1053 −0.1348 −0.0436 0.0000 0.0419 0.1515
ES.H3K4me3 Findpeaks 0.8738 0.8873 −0.1204 −0.1868 −0.0886 −0.0451 0.0000 0.1060
ES.H3K27me3 Findpeaks 1.0000 1.0000 −0.1573 −0.5390 −0.2013 −0.2650 −0.1262 0.0000
MYO.H3k27me3.GM.VDA Fseq 0.7638 0.8421 0.0000 −0.2281 −0.0613 −0.1373 0.1294 −0.0148
MYO.H3k36me3.GM.VDA Fseq 0.6140 0.6355 −0.0819 0.0000 0.1635 0.1397 0.2359 0.2272
MYO.H3k27me3.GM Fseq 0.7931 0.7998 −0.1106 −0.1808 0.0000 −0.0698 0.1206 0.0833
MYO.H3k27me3.MT Fseq 0.7128 0.7752 −0.2216 −0.1397 0.0238 0.0000 0.0962 0.0876
ES.H3K4me3 Fseq 0.9742 0.9995 −0.2815 −0.4974 −0.2062 −0.2723 0.0000 −0.1975
ES.H3K27me3 Fseq 0.8366 0.8831 −0.1939 −0.2641 −0.0833 −0.1531 0.0373 0.0000
MYO.H3k27me3.GM.VDA MACS 0.6583 0.6736 0.0000 −0.0549 −0.1176 −0.1570 0.3139 0.1904
MYO.H3k36me3.GM.VDA MACS 0.6148 0.6247 −0.1247 0.0000 −0.1247 −0.0738 0.2774 0.2205
MYO.H3k27me3.GM MACS 0.5980 0.6061 −0.0139 −0.0147 0.0000 −0.0706 0.2222 0.0697
MYO.H3k27me3.MT MACS 0.5394 0.5553 −0.0553 0.0693 −0.0553 0.0000 0.4136 0.2775
ES.H3K4me3 MACS 0.9630 0.9886 −0.3218 −0.3726 −0.4046 −0.4678 0.0000 −0.1212
ES.H3K27me3 MACS 0.6757 0.8674 −0.2006 −0.2514 −0.2834 −0.3466 0.1212 0.0000
MYO.H3k27me3.GM.VDA PeakSeq 0.6500 0.7064 0.0000 −0.1877 0.0224 −0.0757 −0.2064 0.0436
MYO.H3k36me3.GM.VDA PeakSeq 0.5483 0.5509 0.0989 0.0000 0.1337 0.0164 0.3755 0.1785
MYO.H3k27me3.GM PeakSeq 0.6229 0.7289 −0.0224 −0.2101 0.0000 −0.0982 −0.2289 0.0211
MYO.H3k27me3.MT PeakSeq 0.5590 0.6307 0.0757 −0.1119 0.0982 0.0000 −0.1307 0.1193
ES.H3K4me3 PeakSeq 0.4951 0.9290 −0.2784 −0.3803 −0.2268 −0.3507 0.0000 −0.1707
ES.H3K27me3 PeakSeq 0.7294 0.7583 −0.1077 −0.2096 −0.0560 −0.1800 0.1707 0.0000
MYO.H3k27me3.GM.VDA Qeseq 0.8378 0.8378 0.0000 −0.1656 −0.0387 −0.1059 0.1562 0.0325
MYO.H3k36me3.GM.VDA Qeseq 0.6722 0.6722 0.1656 0.0000 0.1269 0.0597 0.3218 0.1981
MYO.H3k27me3.GM Qeseq 0.7991 0.7991 0.0387 −0.1269 0.0000 −0.0672 0.1949 0.0712
MYO.H3k27me3.MT Qeseq 0.7319 0.7319 0.1059 −0.0597 0.0672 0.0000 0.2621 0.1384
ES.H3K4me3 Qeseq 0.9940 0.9940 −0.1562 −0.3218 −0.1949 −0.2621 0.0000 −0.1237
ES.H3K27me3 Qeseq 0.8703 0.8703 −0.0325 −0.1981 −0.0712 −0.1384 0.1237 0.0000
MYO.H3k27me3.GM.VDA QuEST 0.5011 0.5011 0.0000 −0.0011 −0.0011 −0.0011 0.1685 0.0540
MYO.H3k36me3.GM.VDA QuEST 0.5000 0.5000 0.0011 0.0000 0.0000 0.0000 0.1697 0.0551
MYO.H3k27me3.GM QuEST 0.5000 0.5000 0.0011 0.0000 0.0000 0.0000 0.1696 0.0551
MYO.H3k27me3.MT QuEST 0.5000 0.5000 0.0011 0.0000 0.0000 0.0000 0.1697 0.0551
ES.H3K4me3 QuEST 0.6697 0.6697 −0.1685 −0.1697 −0.1696 −0.1697 0.0000 −0.1146
ES.H3K27me3 QuEST 0.5551 0.5551 −0.0540 −0.0551 −0.0551 −0.0551 0.1146 0.0000
MYO.H3k27me3.GM.VDA RSEG 0.8591 0.8591 0.0000 −0.2374 −0.0600 −0.1237 0.1381 0.0863
MYO.H3k36me3.GM.VDA RSEG 0.6217 0.7516 −0.1824 0.0000 0.0089 0.0866 0.0370 0.1093
MYO.H3k27me3.GM RSEG 0.7991 0.7991 0.0600 −0.1773 0.0000 −0.0637 0.1981 0.1463
MYO.H3k27me3.MT RSEG 0.7354 0.8387 −0.2672 −0.0927 −0.0411 0.0000 0.1273 0.0223
ES.H3K4me3 RSEG 0.9972 0.9972 −0.1381 −0.3754 −0.1981 −0.2618 0.0000 −0.0518
ES.H3K27me3 RSEG 0.9454 0.9469 −0.0878 −0.3252 −0.1478 −0.2115 0.0503 −0.0015
MYO.H3k27me3.GM.VDA SICER 0.5000 0.5000 0.0000 0.1212 0.0000 0.0000 0.4970 0.3853
MYO.H3k36me3.GM.VDA SICER 0.6212 0.7038 −0.2038 0.0000 −0.2038 −0.2038 0.1803 0.2739
MYO.H3k27me3.GM SICER 0.5000 0.5000 0.0000 0.1212 0.0000 0.0000 0.4970 0.3853
MYO.H3k27me3.MT SICER 0.5000 0.7355 −0.2355 −0.1337 −0.2355 0.0000 0.2569 0.1500
ES.H3K4me3 SICER 0.9970 0.9970 −0.4970 −0.3757 −0.4970 −0.4970 0.0000 −0.1117
ES.H3K27me3 SICER 0.8853 0.9777 −0.4777 −0.2739 −0.4777 −0.4777 −0.0936 0.0000
MYO.H3k27me3.GM.VDA SISSRS 0.5089 0.5466 0.0000 −0.0372 −0.0309 −0.0431 0.0860 0.0603
MYO.H3k36me3.GM.VDA SISSRS 0.5002 0.5094 0.0372 0.0000 0.0063 −0.0059 0.1232 0.0975
MYO.H3k27me3.GM SISSRS 0.5010 0.5269 0.0142 −0.0266 0.0000 −0.0225 0.3081 0.1262
MYO.H3k27me3.MT SISSRS 0.5002 0.5068 0.0335 −0.0066 0.0168 0.0000 0.1746 0.1189
ES.H3K4me3 SISSRS 0.5000 0.8350 −0.2939 −0.3347 −0.3081 −0.3306 0.0000 −0.1819
ES.H3K27me3 SISSRS 0.5000 0.6533 −0.1119 −0.1478 −0.1288 −0.1486 0.1517 0.0000
MYO.H3k27me3.GM.VDA SWEMBL 0.8124 0.9128 0.0000 −0.2938 −0.1130 −0.1766 0.0426 −0.0273
MYO.H3k36me3.GM.VDA SWEMBL 0.6037 0.6190 0.2938 0.0000 0.1807 0.1172 0.3364 0.2665
MYO.H3k27me3.GM SWEMBL 0.7998 0.7998 0.0127 −0.1960 0.0000 −0.0635 0.1034 0.0750
MYO.H3k27me3.MT SWEMBL 0.7362 0.7362 0.0762 −0.1325 0.0635 0.0000 0.1669 0.1385
ES.H3K4me3 SWEMBL 0.9032 0.9741 −0.1603 −0.3691 −0.1743 −0.2378 0.0000 −0.0965
ES.H3K27me3 SWEMBL 0.8747 0.8855 0.0273 −0.2665 −0.0857 −0.1493 0.0699 0.0000
MYO.H3k27me3.GM.VDA TPIC 0.8025 0.8811 0.0000 −0.2738 −0.0861 −0.1745 0.0830 −0.0477
MYO.H3k36me3.GM.VDA TPIC 0.6200 0.6200 0.1825 0.0000 0.1793 0.1155 0.3614 0.2407
MYO.H3k27me3.GM TPIC 0.7993 0.8042 −0.0253 −0.1976 0.0000 −0.0812 0.1599 0.0291
MYO.H3k27me3.MT TPIC 0.7355 0.7355 0.0670 −0.1155 0.0637 0.0000 0.2458 0.1251
ES.H3K4me3 TPIC 0.9814 0.9814 −0.1789 −0.3614 −0.1821 −0.2458 0.0000 −0.1207
ES.H3K27me3 TPIC 0.8607 0.8607 −0.0582 −0.2407 −0.0614 −0.1251 0.1207 0.0000
MYO.H3k27me3.GM.VDA W-ChiPeaks 0.5085 0.5136 0.0000 −0.0136 −0.0030 −0.0125 0.3147 0.2409
MYO.H3k36me3.GM.VDA W-ChiPeaks 0.5000 0.5000 0.0085 0.0000 0.0046 0.0015 0.3373 0.2185
MYO.H3k27me3.GM W-ChiPeaks 0.5046 0.5140 −0.0035 −0.0140 0.0000 −0.0045 0.3227 0.2881
MYO.H3k27me3.MT W-ChiPeaks 0.5015 0.5100 0.0000 −0.0100 0.0029 0.0000 0.3208 0.2921
ES.H3K4me3 W-ChiPeaks 0.8373 0.8458 −0.3354 −0.3458 −0.3401 −0.3386 0.0000 −0.0558
ES.H3K27me3 W-ChiPeaks 0.7185 0.8020 −0.2921 −0.3020 −0.2892 −0.2921 0.0288 0.0000