PFM families for TRANSFAC cores Format: Index Matrix1 (Factor name) Matrix2 (Factor name) etc. aveS minS aveS = average similarity in family minS = minimum similarity in family 1 M00097 (Pax-6) M00187 (USF) M00327 (Pax-3) 0.0749985333333333 0.0492138 2 M00187 (USF) M00322 (c-Myc/Max) M00400 (ABF1) 0.128746333333333 0.081123 3 M00187 (USF) M00221 (SREBP-1) M00717 (Pax-8) 0.1751163 0.0682869 4 M00134 (HNF-4) M00155 (ARP-1) M00242 (PPARalpha/RXR-alpha) M00275 (Mat1-Mc) M00638 (HNF-4alpha) M00671 (TCF-4) M00745 (LEF-1) M00762 (direct repeat 1) M00764 (HNF-4 direct repeat 1) 0.6408165 0.248818 5 M00017 (ATF) M00036 (v-Jun) M00039 (CREB) M00177 (CREB) M00178 (CREB) M00338 (ATF) M00356 (bZIP910) M00357 (bZIP910) M00358 (bZIP911) M00359 (bZIP911) M00483 (ATF6) M00801 (CREB) 0.940041651515151 0.526055 6 M00113 (CREB) M00114 (Tax/CREB) M00697 (HBP-1b) 0.726451333333333 0.676149 7 M00367 (HBP-1a) M00369 (TAF-1) M00370 (CPRF-3) M00371 (CPRF-2) M00372 (O2) M00653 (OCSBF-1) 0.9738852 0.90091 8 M00006 (MEF-2) M00403 (aMEF-2) M00405 (MEF-2) 0.838880333333333 0.750025 9 M00035 (v-Maf) M00037 (NF-E2) M00304 (Dde box) M00312 (Bel-1) M00361 (CDC5) M00374 (O2) 0.361111773333333 0.0744255 10 M00105 (CDP CR3) M00305 (HAP1) M00488 (DREF) 0.293097 0.111545 11 M00064 (PHO4) M00368 (CPRF-1) M00401 (ABF1) M00440 (CG1) M00441 (GBF) M00788 (EmBP-1b) 0.989086933333333 0.836304 12 M00073 (deltaEF1) M00150 (Brachyury) M00413 (AREB6) 0.727979 0.449216 13 M00733 (SMAD-4) M00792 (SMAD) 0.377067 0.377067 14 M00317 (Poly A) M00733 (SMAD-4) 0.0716319 0.0716319 15 M00118 (c-Myc/Max) M00119 (Max) M00121 (USF) M00434 (PIF3) M00435 (PIF3) M00442 (ABF) M00539 (Arnt) M00615 (c-Myc/Max) 0.882726071428571 0.502915 16 M00055 (N-Myc) M00251 (XBP-1) M00538 (HTF) M00799 (Myc) 0.2572225 0.123311 17 M00093 (BR-C Z3) M00438 (ARF) 0.0489482 0.0489482 18 M00093 (BR-C Z3) M00219 (MYB.Ph3) 0.173198 0.173198 19 M00081 (Evi-1) M00093 (BR-C Z3) M00439 (C1) 0.153534433333333 0.070493 20 M00446 (Spz1) M00695 (ETF) 0.0953415 0.0953415 21 M00196 (Sp1) M00695 (ETF) 0.368383 0.368383 22 M00008 (Sp1) M00255 (GC) M00695 (ETF) 0.0863604 0.0591458 23 M00418 (TGIF) M00419 (MEIS1) M00420 (MEIS1A/HOXA9) M00421 (MEIS1B/HOXA9) 0.635218833333333 0.307128 24 M00716 (ZF5) M00807 (EGR) 0.230635 0.230635 25 M00333 (ZF5) M00716 (ZF5) 0.626884 0.626884 26 M00380 (Pax-4) M00404 (MADS-B) M00632 (GATA-4) M00692 (Antp) 0.319427733333333 0.0692644 27 M00143 (BSAP) M00321 (Muscle initiator) M00323 (Muscle initiator sequences-19) M00328 (Pax-8) 0.439130333333333 0.124674 28 M00185 (NF-Y) M00288 (HAP2/3/4) M00309 (ACAAT) M00687 (alpha-CP1) M00775 (NF-Y) 0.8762831 0.605291 29 M00161 (Oct-1) M00195 (Oct-1) 0.619175 0.619175 30 M00324 (Muscle initiator sequences-20) M00325 (neural-restr.-silencer-element) 0.0981043 0.0981043 31 M00472 (FOXO4) M00473 (FOXO1) 0.924411 0.924411 32 M00098 (Pax-2) M00626 (RFX1 (EF-C)) M00703 (TAF) 0.429857666666667 0.325842 33 M00109 (C/EBPbeta) M00116 (C/EBPalpha) M00190 (C/EBP) M00621 (C/EBPdelta) 0.19288305 0.0586711 34 M00236 (Arnt) M00366 (EmBP-1) M00466 (HIF-1) M00797 (HIF-1) 0.9206115 0.802742 35 M00091 (BR-C Z1) M00432 (TTF1) M00794 (TTF-1) 0.229733533333333 0.0563336 36 M00432 (TTF1) M00526 (GCNF) 0.346961 0.346961 37 M00373 (Pax-4) M00432 (TTF1) 0.164493 0.164493 38 M00087 (Ik-2) M00141 (Lyf-1) M00264 (Staf) M00480 (LUN-1) 0.2513335 0.103959 39 M00262 (Staf) M00264 (Staf) 0.343141 0.343141 40 M00425 (E2F) M00426 (E2F) M00430 (E2F-1) 0.816572666666667 0.719728 41 M00392 (AGL3) M00393 (AGL3) M00640 (HOXA4) 0.217398 0.112443 42 M00490 (Bach2) M00495 (Bach1) 0.102554 0.102554 43 M00138 (Oct-1) M00795 (Octamer) 0.103048 0.103048 44 M00104 (CDP CR1) M00639 (HNF-6) 0.072472 0.072472 45 M00033 (p300) M00702 (SPF1) 0.0568915 0.0568915 46 M00463 (POU3F2) M00802 (Pit-1) 0.152705 0.152705 47 M00045 (E4BP4) M00502 (TEIL) 0.0610862 0.0610862 48 M00311 (ATATA) M00485 (Nkx2-2) 0.0896675 0.0896675 49 M00702 (SPF1) M00754 (ZAP1) 0.0508385 0.0508385 50 M00192 (GR) M00481 (AR) 0.112148 0.112148 51 M00033 (p300) M00048 (ADR1) 0.0461026 0.0461026 52 M00433 (Hmx3) M00485 (Nkx2-2) 0.108831 0.108831 53 M00104 (CDP CR1) M00106 (CDP CR3+HD) 0.0586521 0.0586521 54 M00731 (Osf2) M00751 (AML1) M00769 (AML) 0.913895666666667 0.861188 55 M00127 (GATA-1) M00349 (GATA-2) 0.465089 0.465089 56 M00518 (PPARalpha/RXR-alpha) M00631 (FXR) M00647 (LXR) M00766 (LXR direct repeat 4) M00767 (FXR inverted repeat 1) 0.720692 0.382025 57 M00279 (MIF-1) M00280 (RFX1) M00281 (RFX1) 0.706104 0.559156 58 M00125 (MCM1) M00257 (RREB-1) 0.13295 0.13295 59 M00257 (RREB-1) M00690 (AP-3) 0.0729013 0.0729013 60 M00257 (RREB-1) M00501 (ANT) 0.0756693 0.0756693 61 M00257 (RREB-1) M00528 (PPAR) 0.393532 0.393532 62 M00271 (AML-1a) M00722 (core-binding factor) 0.822498 0.822498 63 M00449 (Zic2) M00722 (core-binding factor) 0.643547 0.643547 64 M00183 (c-Myb) M00461 (Ovo) M00773 (MYB) 0.370224 0.101153 65 M00241 (Nkx2-5) M00377 (Pax-4) M00489 (Nkx6-2) M00696 (En) 0.652185 0.318102 66 M00173 (AP-1) M00174 (AP-1) M00188 (AP-1) M00517 (AP-1) M00681 (WRKY) 0.5940522 0.287091 67 M00099 (S8) M00248 (Oct-1) M00416 (Cart-1) M00437 (CHX10) 0.328015833333333 0.148264 68 M00078 (Evi-1) M00079 (Evi-1) M00080 (Evi-1) M00082 (Evi-1) 0.502019166666667 0.278444 69 M00021 (Kr) M00110 (Elf-1) M00630 (FOXM1) M00633 (GBF) M00670 (TCF-1(P)) 0.3348232 0.115024 70 M00044 (Sn) M00725 (HP1 site factor) 0.304529 0.304529 71 M00072 (CP2) M00725 (HP1 site factor) 0.421983 0.421983 72 M00043 (dl) M00052 (NF-kappaB (p65)) M00225 (STAT3) M00259 (STAT) M00302 (NF-AT) 0.40563608 0.0491208 73 M00111 (CF1 / USP) M00158 (COUP-TF / HNF-4) M00191 (ER) M00515 (PPARG) 0.26038515 0.0715599 74 M00086 (Ik-1) M00088 (Ik-3) M00194 (NF-kappaB) 0.279334 0.074629 75 M00115 (Tax/CREB) M00179 (CRE-BP1) M00694 (E4F1) 1 1 76 M00171 (Adf-1) M00389 (FACB) M00629 (Eve) 0.303904 0.116973 77 M00042 (Sox-5) M00160 (SRY) M00276 (Mat1-Mc) M00410 (SOX-9) M00728 (ROX1) 0.52674209 0.0888879 78 M00310 (APOLYA) M00318 (Lentiviral Poly A) M00503 (ATHB-5) 0.469034666666667 0.257429 79 M00457 (STAT5A (homodimer)) M00459 (STAT5B (homodimer)) M00500 (STAT6) 0.2397619 0.0636937 80 M00339 (c-Ets-1) M00340 (c-Ets-2) M00771 (ETS) 0.799949333333333 0.690147 81 M00067 (Hairy) M00139 (AhR) M00235 (AhR/Arnt) M00237 (AhR/Arnt) M00778 (AhR) 0.7681968 0.425243 82 M00131 (HNF-3beta) M00724 (HNF-3alpha) M00791 (HNF-3) M00809 (FOX) 0.476026333333333 0.280105 83 M00313 (GEN_INI) M00314 (GEN_INI) M00315 (GEN_INI) 1 1 84 M00022 (Hb) M00734 (CIZ) 0.218828 0.218828 85 M00100 (CdxA) M00145 (Brn-2) M00408 (MADS-A) M00423 (FOXJ2) M00445 (Xvent-1) 0.27399999 0.0827545 86 M00234 (Su(H)) M00479 (Alfin1) 0.516997 0.516997 87 M00102 (CDP) M00103 (Clox) 0.685583 0.685583 88 M00007 (Elk-1) M00046 (GCR1) M00108 (NRF-2) M00337 (GCR1) M00341 (GABP) M00648 (MAF) M00655 (PEA3) M00658 (PU.1) M00743 (c-Ets-1 68) 0.78404975 0.253411 89 M00182 (GBP) M00375 (TGA1b) M00376 (TGA1a) M00660 (RITA-1) 0.929937833333333 0.860059 90 M00026 (RSRFC4) M00092 (BR-C Z2) M00407 (RSRFC4) 0.424138333333333 0.190499 91 M00396 (En-1) M00622 (C/EBPgamma) M00678 (Tel-2) M00689 (unc-86) M00704 (TEF-1) 0.3415045 0.162319 92 M00448 (Zic1) M00506 (LIM1) M00665 (Sp3) M00698 (HEB) M00706 (TFII-I) M00720 (CAC-binding protein) 0.326834533333333 0.129943 93 M00056 (myogenin / NF- 1) M00193 (NF-1) M00247 (PacC) M00806 (NF-1) 0.605021666666667 0.279833 94 M00024 (E2F) M00062 (IRF-1) M00063 (IRF-2) M00120 (dl) 0.718624833333333 0.302779 95 M00511 (ERR alpha) M00763 (PPAR direct repeat 1) M00765 (COUP direct repeat 1) 0.405588233333333 0.0902467 96 M00029 (HSF) M00167 (HSF) M00168 (HSF) 1 1 97 M00009 (Ttk 69K) M00032 (c-Ets-1(p54)) M00531 (NERF1a) 0.700836333333333 0.461339 98 M00084 (MZF1) M00154 (STRE) M00308 (STRE) 0.518568333333333 0.138862 99 M00230 (Skn-1) M00417 (ATHB-9) 1 1 100 M00240 (Nkx2-5) M00451 (NKX3A) 0.23891 0.23891 101 M00240 (Nkx2-5) M00747 (IRF1) 0.408982 0.408982 102 M00240 (Nkx2-5) M00468 (AP-2rep) 0.21086 0.21086 103 M00469 (AP-2alpha) M00470 (AP-2gamma) 0.323709 0.323709 104 M00274 (STE11) M00411 (HNF-4alpha1) M00805 (LEF1) 0.671903 0.494952 105 M00289 (HFH-3) M00422 (FOXJ2) 0.909971 0.909971 106 M00476 (FOXO4) M00477 (FOXO3) 1 1 107 M00346 (GATA-1) M00347 (GATA-1) M00348 (GATA-2) M00350 (GATA-3) M00487 (mtTFA) 0.7579236 0.429918 108 M00186 (SRF) M00810 (SRF) 0.766696 0.766696 109 M00319 (MEF-3) M00619 (Alx-4) M00684 (XPF-1) 0.658906 0.488359 110 M00129 (HFH-1) M00290 (Freac-2) M00292 (Freac-4) 0.761390333333333 0.712837 111 M00075 (GATA-1) M00076 (GATA-2) M00077 (GATA-3) 0.234258333333333 0.110291 112 M00258 (ISRE) M00415 (AREB6) M00641 (HSF) M00699 (ICSBP) 0.579574333333333 0.431198 113 M00012 (CF2-II) M00013 (CF2-II) 0.963327 0.963327 114 M00146 (HSF1) M00147 (HSF2) M00447 (AR) M00460 (STAT5A (homotetramer)) 0.2621245 0.107577 115 M00316 (Imperfect Hogness/Goldberg BOX) M00352 (Dof1) M00355 (PBF) 0.3909262 0.0967056 116 M00189 (AP-2) M00306 (LEU3) M00634 (GCM) M00752 (PDR3) 0.207569266666667 0.0633676 117 M00156 (RORalpha1) M00157 (RORalpha2) M00239 (v-ErbA) M00512 (PPARG) 0.981292666666667 0.887756 118 M00664 (STE12) M00772 (IRF) 0.961995 0.961995 119 M00041 (CRE-BP1/c-Jun) M00443 (Opaque2) M00691 (ATF-1) 0.148473266666667 0.0662348 120 M00015 (ABF1) M00691 (ATF-1) 0.121814 0.121814 121 M00231 (MEF-2) M00232 (MEF-2) M00233 (MEF-2) M00406 (MEF-2) 0.5544695 0.278386 122 M00122 (USF) M00123 (c-Myc/Max) M00220 (SREBP-1) M00796 (USF) 0.211005483333333 0.0911689 123 M00184 (MyoD) M00804 (E2A) 0.644806 0.644806 124 M00427 (E2F) M00428 (E2F-1) M00431 (E2F-1) 0.608338666666667 0.496005 125 M00378 (Pax-4) M00450 (Zic3) M00721 (CACCC-binding factor) M00749 (SREBP-1) M00753 (RCS1) M00776 (SREBP) 0.6637578 0.176944 126 M00051 (NF-kappaB (p50)) M00083 (MZF1) M00261 (Olf-1) 0.426828 0.270218 127 M00507 (TRAB1) M00654 (OSBZ8) M00726 (USF2) 0.736566333333333 0.470433 128 M00334 (D-Type LTRs) M00732 (CAT8) 1 1 129 M00003 (v-Myb) M00227 (v-Myb) M00326 (Pax-1) 0.773976 0.410074 130 M00065 (Tal-1beta/E47) M00070 (Tal-1beta/ITF-2) 0.733469 0.733469 131 M00165 (HSF) M00166 (HSF) 1 1 132 M00014 (repressor of CAR1 expression) M00047 (qa-1F) 0.139459 0.139459 133 M00010 (O2) M00708 (Vmw65) M00710 (Zen) 0.656731666666667 0.358108 134 M00456 (FAC1) M00798 (MYBAS1) 0.046348 0.046348 135 M00260 (HLF) M00798 (MYBAS1) 0.0849244 0.0849244 136 M00004 (c-Myb) M00798 (MYBAS1) 0.323072 0.323072 137 M00238 (Barbie Box) M00353 (Dof2) M00354 (Dof3) 0.901881333333333 0.858886 138 M00016 (E74A) M00025 (Elk-1) M00074 (c-Ets-1(p54)) 0.383281333333333 0.195724 139 M00294 (HFH-8) M00474 (FOXO1) M00475 (DAF-16) 0.532687666666667 0.303962 140 M00513 (ATF3) M00514 (ATF4) 0.72974 0.72974 141 M00736 (E2F-1/DP-1) M00737 (E2F-1/DP-2) M00739 (E2F-4/DP-2) 0.594095333333333 0.584703 142 M00652 (Nrf-1) M00662 (SGF-3) 0.0777969 0.0777969 143 M00652 (Nrf-1) M00711 (Zta) 0.0652731 0.0652731 144 M00650 (MTF-1) M00652 (Nrf-1) 0.31489 0.31489 145 M00053 (c-Rel) M00453 (IRF-7) M00496 (STAT1) M00750 (HMG) 0.21785195 0.059705 146 M00059 (YY1) M00069 (YY1) M00651 (NF-muE1) M00793 (YY1) 0.572766166666667 0.190376 147 M00005 (AP-4) M00175 (AP-4) M00176 (AP-4) M00644 (LBP-1) 0.897699666666667 0.685632 148 M00163 (HSF) M00164 (HSF) 1 1 149 M00066 (Tal-1alpha/E47) M00532 (RP58) 0.76882 0.76882 150 M00126 (GATA-1) M00128 (GATA-1) M00142 (NIT2) M00278 (Lmo2 complex) 0.728798166666667 0.258298 151 M00107 (E2) M00181 (E2) 0.613446 0.613446 152 M00229 (Skn-1) M00284 (TCF11/MafG) M00285 (TCF11) 0.506899666666667 0.270708 153 M00058 (HEN1) M00068 (HEN1) 0.296101 0.296101 154 M00018 (Ubx) M00023 (Hox-1.3) M00436 (IPF1) 0.900706666666667 0.776352 155 M00169 (HSF) M00170 (HSF) 1 1 156 M00050 (E2F) M00516 (E2F) M00738 (E2F-4/DP-1) M00740 (Rb/E2F-1/DP-1) 0.775934333333333 0.453974