Table 3.
Comparison of optimal motifs for TFs common to MatBase, Transfac and the union of public databases
| ENCODE/funcgen | MatBase | Transfac Prof. | Jaspar vert. | Hocomoco | HT-Selex | SwissRegulon | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| TF name | AUC | matrix name | AUC | matrix name | AUC | matrix name | AUC | matrix name | AUC | matrix name | AUC | matrix name |
| ATF3 | 0.710 | V$CREB.02 | 0.693 | M00981 | – | – | 0.694 | M00015 | – | – | – | – |
| Ap2alpha | 0.809 | V$AP2.02 | 0.807 | M01045 | 0.816 | MA0003.2 | 0.777 | M00004 | 0.779 | selex292 | 0.754 | TFAP2A,C.p2 |
| Ap2gamma | 0.799 | V$AP2.02 | 0.765 | M00470 | 0.792 | MA0524.1 | 0.781 | M00006 | 0.784 | selex298 | 0.751 | TFAP2A,C.p2 |
| BHLHE40 | 0.947 | V$BHLHB2.01 | 0.799 | M01034 | 0.885 | MA0464.1 | 0.955 | M00022 | 0.958 | selex316 | 0.917 | ARNT_ARNT2_BHLHB2_ |
| MAX_MYC_USF1.p2 | ||||||||||||
| CTCF | 0.929 | V$CTCF.04 | 0.931 | M01259 | 0.942 | MA0139.1 | 0.940 | M00045 | 0.922 | selex2 | 0.934 | CTCF.p2 |
| Cfos | 0.751 | V$AP1.01 | 0.759 | M00517 | 0.744 | MA0476.1 | 0.760 | M00093 | – | – | 0.742 | FOS_FOSB,L1_JUNB,D.p2 |
| Cjun | 0.814 | V$AP1.01 | 0.820 | M00925 | 0.799 | MA0099.1 | 0.827 | M00183 | – | – | 0.570 | JUN.p2 |
| Cmyc | 0.700 | V$CMYC.01 | 0.685 | M00322 | 0.702 | MA0147.1 | 0.690 | M00216 | – | – | 0.659 | ARNT_ARNT2_BHLHB2_ |
| MAX_MYC_USF1.p2 | ||||||||||||
| E2F1 | 0.802 | V$E2F3.01 | 0.764 | M00938 | 0.753 | MA0024.2 | 0.694 | M00052 | 0.723 | selex750 | 0.674 | E2F1..5.p2 |
| E2F4 | 0.682 | V$E2F4.01 | 0.678 | M00920 | 0.689 | MA0470.1 | 0.650 | M00055 | 0.502 | selex753 | 0.654 | E2F1..5.p2 |
| E2F6 | 0.698 | V$E2F4.01 | 0.435 | M01252 | 0.653 | MA0471.1 | 0.681 | M00057 | – | – | – | – |
| EBF | 0.740 | V$EBF1.01 | 0.736 | M01871 | 0.721 | MA0154.2 | 0.746 | M00037 | 0.751 | selex79 | 0.692 | EBF1.p2 |
| ELF1 | 0.862 | V$ELK1.03 | 0.835 | M02053 | 0.800 | MA0473.1 | 0.832 | M00065 | 0.836 | selex81 | 0.797 | ELF1,2,4.p2 |
| ETS1 | 0.765 | V$ELK3.01 | 0.753 | M02063 | 0.680 | MA0098.1 | 0.708 | M00082 | 0.765 | selex100 | 0.683 | ETS1,2.p2 |
| Egr1 | 0.831 | V$EGR1.01 | 0.848 | M01972 | 0.822 | PB0010.1 | 0.844 | M00060 | 0.853 | selex3 | 0.841 | EGR1..3.p2 |
| FOSL1 | 0.885 | V$AP1.02 | 0.890 | M00517 | 0.890 | MA0477.1 | 0.865 | M00091 | – | – | 0.881 | FOS_FOSB,L1_JUNB,D.p2 |
| FOSL2 | 0.877 | V$AP1.01 | 0.870 | M00925 | 0.865 | MA0478.1 | 0.885 | M00092 | – | – | 0.852 | FOSL2.p2 |
| FOXA1 | 0.763 | V$FREAC4.01 | 0.826 | M01261 | 0.832 | MA0148.3 | 0.808 | M00094 | – | – | – | – |
| FOXA2 | 0.759 | V$FREAC4.01 | 0.735 | M02014 | 0.834 | MA0047.2 | 0.816 | M00095 | – | – | 0.834 | FOXA2.p3 |
| Gabp | 0.873 | V$ELK1.03 | 0.867 | M02074 | 0.879 | MA0062.2 | 0.876 | M00116 | 0.871 | selex116 | 0.870 | ELK1,4_GABPA,B1.p3 |
| Gata1 | 0.711 | V$GATA5.01 | 0.685 | M00203 | 0.683 | MA0035.3 | 0.697 | M00117 | – | – | 0.479 | GATA1..3.p2 |
| Gata2 | 0.853 | V$GATA2.03 | 0.834 | M00789 | 0.834 | MA0036.2 | 0.843 | M00118 | – | – | 0.538 | GATA1..3.p2 |
| HNF4A | 0.801 | V$HNF4.01 | 0.838 | M02220 | 0.847 | MA0114.2 | 0.850 | M00147 | 0.837 | selex673 | 0.809 | HNF4A_NR2F1,2.p2 |
| HNF4G | 0.864 | V$HNF4.01 | 0.811 | M00764 | 0.898 | MA0484.1 | 0.788 | M00148 | – | – | – | – |
| IRF4 | 0.669 | V$ISRE.01 | 0.641 | M00772 | 0.648 | PB0034.1 | 0.603 | M00174 | 0.665 | selex148 | – | – |
| Junb | 0.912 | V$AP1.01 | 0.912 | M00925 | 0.920 | MA0490.1 | 0.911 | M00181 | – | – | 0.900 | FOS_FOSB,L1_JUNB,D.p2 |
| Jund | 0.820 | V$AP1.01 | 0.823 | M00925 | 0.817 | MA0491.1 | 0.827 | M00182 | – | – | 0.805 | FOS_FOSB,L1_JUNB,D.p2 |
| MEF2A | 0.643 | V$MEF2.02 | 0.650 | M00231 | 0.653 | MA0052.2 | 0.616 | M00204 | 0.615 | selex156 | 0.604 | MEF2A,B,C,D.p2 |
| MEF2C | 0.721 | V$MEF2.02 | 0.682 | M00941 | 0.719 | MA0497.1 | 0.664 | M00205 | – | – | 0.669 | MEF2A,B,C,D.p2 |
| Max | 0.738 | V$CMYC.01 | 0.703 | M00322 | 0.700 | PB0043.1 | 0.720 | M00199 | 0.730 | selex326 | 0.711 | ARNT_ARNT2_BHLHB2_ |
| MAX_MYC_USF1.p2 | ||||||||||||
| NFKB | 0.896 | V$NFKAPPAB65.02 | 0.891 | M00774 | 0.878 | MA0105.3 | 0.872 | M00235 | 0.776 | selex189 | 0.861 | NFKB1_REL_RELA.p2 |
| NR4A1 | 0.512 | V$NBRE.01 | 0.492 | M01217 | – | – | 0.542 | M00259 | – | – | – | – |
| Nanog | 0.560 | V$HOXA2.01 | 0.631 | M01247 | – | – | 0.556 | M00221 | – | – | 0.630 | NANOGmouse.p2 |
| Nfe2 | 0.855 | V$NFE2.01 | 0.846 | M00037 | 0.877 | MA0501.1 | 0.882 | M00231 | 0.771 | selex392 | 0.835 | NFE2.p2 |
| Nrf1 | 0.951 | V$NRF1.01 | 0.969 | M00652 | 0.963 | MA0506.1 | 0.973 | M00264 | 0.977 | selex194 | 0.968 | NRF1.p2 |
| Nrsf | 0.838 | V$NRSF.02 | 0.879 | M01256 | 0.850 | MA0138.2 | 0.854 | M00316 | – | – | 0.847 | REST.p3 |
| POU2F2 | 0.513 | V$OCT1.02 | 0.498 | M00210 | 0.481 | MA0507.1 | 0.504 | M00290 | 0.503 | selex232 | 0.503 | POU2F1..3.p2 |
| POU5F1 | 0.868 | V$OCT3_4.02 | 0.857 | M01125 | 0.881 | MA0142.1 | 0.874 | M00294 | – | – | 0.857 | POU5F1_SOX2dimer.p2 |
| PU1 | 0.932 | V$SPI1.05 | 0.884 | M01203 | 0.914 | MA0080.3 | 0.922 | M00350 | 0.860 | selex123 | 0.884 | SPI1.p2 |
| Pax5 | 0.613 | V$PAX5.01 | 0.613 | M00143 | 0.713 | MA0014.2 | 0.729 | M00274 | 0.768 | selex200 | 0.606 | PAX5.p2 |
| Pbx3 | 0.739 | V$PBX1_MEIS1.01 | 0.546 | M00998 | – | – | 0.758 | M00280 | – | – | – | – |
| RXRA | 0.714 | V$PPARG.03 | 0.608 | M02272 | 0.707 | MA0065.1 | 0.693 | M00326 | 0.731 | selex710 | 0.720 | RXRG_dimer.p3 |
| SP1 | 0.559 | V$SP1.03 | 0.552 | M00932 | 0.561 | MA0079.3 | 0.555 | M00346 | 0.547 | selex29 | 0.551 | SP1.p2 |
| SP2 | 0.711 | V$SP4.01 | 0.719 | M01783 | 0.726 | MA0516.1 | 0.676 | M00347 | – | – | – | – |
| Srf | 0.681 | V$SRF.05 | 0.693 | M00186 | 0.661 | MA0083.1 | 0.657 | M00355 | 0.657 | selex159 | 0.656 | SRF.p3 |
| Tcf12 | 0.723 | V$ASCL2.01 | 0.679 | M00698 | 0.712 | MA0521.1 | 0.703 | M00152 | – | – | 0.574 | TAL1_TCF3,4,12.p2 |
| Tr4 | 0.601 | V$HNF4.01 | 0.644 | M01776 | 0.652 | MA0504.1 | 0.623 | M00256 | 0.611 | selex676 | – | – |
| USF1 | 0.947 | V$USF1.02 | 0.936 | M00121 | 0.903 | MA0093.2 | 0.945 | M00396 | 0.935 | selex352 | 0.932 | ARNT_ARNT2_BHLHB2_ |
| MAX_MYC_USF1.p2 | ||||||||||||
| Yy1 | 0.778 | V$YY1.03 | 0.723 | M02044 | 0.713 | MA0095.2 | 0.735 | M00394 | 0.756 | selex33 | 0.657 | YY1.p2 |
| ZBTB33 | 0.489 | V$KAISO.01 | 0.517 | M01119 | 0.881 | MA0527.1 | 0.749 | M00184 | – | – | – | – |
| ZBTB7A | 0.699 | V$ZF9.01 | 0.682 | M01100 | – | – | 0.640 | M00404 | 0.632 | selex37 | – | – |
| ZEB1 | 0.766 | V$ZEB1.01 | 0.689 | M00414 | 0.752 | MA0103.2 | 0.686 | M00409 | – | – | 0.734 | ZEB1.p2 |
| Znf263 | 0.685 | V$ZNF263.01 | 0.762 | M01587 | 0.653 | MA0528.1 | – | – | – | – | – | – |
For each TF the motif with the highest AUC from each database is presented. The best motifs from all databases and the corresponding AUC are bolded (note that for FOXA2 motifs from Jaspar and SwissRegulon are both optimal). AUC are calculated with respect to negative sequences composed of flanks of ChIP-seq peaks.