PFM families for TRANSFAC extended cores Format: Index Matrix1 (Factor name) Matrix2 (Factor name) etc. aveS minS aveS = average similarity in family minS = minimum similarity in family 1 M00134 (HNF-4) M00638 (HNF-4alpha) M00671 (TCF-4) M00745 (LEF-1) M00764 (HNF-4 direct repeat 1) 0.6637755 0.396933 2 M00064 (PHO4) M00368 (CPRF-1) M00400 (ABF1) M00401 (ABF1) M00440 (CG1) M00441 (GBF) M00788 (EmBP-1b) 0.984409904761905 0.836304 3 M00356 (bZIP910) M00358 (bZIP911) M00359 (bZIP911) 1 1 4 M00113 (CREB) M00114 (Tax/CREB) M00360 (Pax-3) M00697 (HBP-1b) M00801 (CREB) 0.5574021 0.183842 5 M00182 (GBP) M00367 (HBP-1a) M00369 (TAF-1) M00370 (CPRF-3) M00371 (CPRF-2) M00372 (O2) M00375 (TGA1b) M00376 (TGA1a) M00653 (OCSBF-1) M00660 (RITA-1) 0.911741844444444 0.665464 6 M00403 (aMEF-2) M00404 (MADS-B) M00405 (MEF-2) 0.890795666666667 0.672387 7 M00035 (v-Maf) M00037 (NF-E2) M00312 (Bel-1) M00361 (CDC5) 0.43651735 0.0869991 8 M00017 (ATF) M00036 (v-Jun) M00039 (CREB) M00041 (CRE-BP1/c-Jun) M00177 (CREB) M00178 (CREB) M00338 (ATF) M00357 (bZIP910) M00483 (ATF6) 0.947644083333333 0.747064 9 M00049 (GAL4) M00501 (ANT) 0.0830465 0.0830465 10 M00159 (C/EBP) M00624 (DBP) 0.106941 0.106941 11 M00172 (AP-1) M00327 (Pax-3) 0.0966719 0.0966719 12 M00087 (Ik-2) M00480 (LUN-1) 0.103959 0.103959 13 M00093 (BR-C Z3) M00219 (MYB.Ph3) 0.173198 0.173198 14 M00105 (CDP CR3) M00488 (DREF) 0.169043 0.169043 15 M00433 (Hmx3) M00485 (Nkx2-2) 0.108831 0.108831 16 M00650 (MTF-1) M00652 (Nrf-1) 0.31489 0.31489 17 M00311 (ATATA) M00485 (Nkx2-2) 0.0896675 0.0896675 18 M00104 (CDP CR1) M00106 (CDP CR3+HD) 0.162599 0.162599 19 M00344 (RAV1) M00413 (AREB6) 0.334023 0.334023 20 M00060 (Sn) M00073 (deltaEF1) M00150 (Brachyury) M00413 (AREB6) 0.6036775 0.161578 21 M00118 (c-Myc/Max) M00119 (Max) M00121 (USF) M00434 (PIF3) M00435 (PIF3) M00442 (ABF) M00539 (Arnt) M00615 (c-Myc/Max) 0.882726071428571 0.502915 22 M00055 (N-Myc) M00251 (XBP-1) M00538 (HTF) M00799 (Myc) 0.321709166666667 0.183875 23 M00418 (TGIF) M00419 (MEIS1) M00420 (MEIS1A/HOXA9) M00421 (MEIS1B/HOXA9) 0.635218833333333 0.307128 24 M00004 (c-Myb) M00479 (Alfin1) M00807 (EGR) 0.400759 0.248416 25 M00081 (Evi-1) M00632 (GATA-4) M00635 (GT-1) 0.467147333333333 0.21142 26 M00185 (NF-Y) M00288 (HAP2/3/4) M00309 (ACAAT) M00687 (alpha-CP1) M00775 (NF-Y) 0.8762831 0.605291 27 M00091 (BR-C Z1) M00138 (Oct-1) M00161 (Oct-1) M00195 (Oct-1) M00445 (Xvent-1) M00795 (Octamer) 0.432425266666667 0.134658 28 M00323 (Muscle initiator sequences-19) M00324 (Muscle initiator sequences-20) 1 1 29 M00472 (FOXO4) M00473 (FOXO1) 0.924411 0.924411 30 M00098 (Pax-2) M00626 (RFX1 (EF-C)) M00679 (Tll) M00703 (TAF) 0.27426185 0.0741601 31 M00249 (CHOP-C/EBPalpha) M00621 (C/EBPdelta) 0.183607 0.183607 32 M00236 (Arnt) M00366 (EmBP-1) M00399 (ABF1) M00466 (HIF-1) M00797 (HIF-1) 0.9345545 0.802742 33 M00057 (COMP1) M00325 (neural-restr.-silencer-element) M00374 (O2) M00390 (FACB) 0.129049133333333 0.0817083 34 M00325 (neural-restr.-silencer-element) M00388 (FACB) 0.224773 0.224773 35 M00090 (Abd-B) M00465 (POU6F1) M00744 (POU1F1) 0.3393246 0.0814738 36 M00141 (Lyf-1) M00257 (RREB-1) M00528 (PPAR) 0.482164333333333 0.393532 37 M00141 (Lyf-1) M00264 (Staf) M00777 (STAT) 0.368461 0.190301 38 M00426 (E2F) M00427 (E2F) M00428 (E2F-1) M00431 (E2F-1) 0.658961333333333 0.496005 39 M00223 (STATx) M00234 (Su(H)) M00492 (STAT1) M00497 (STAT3) 0.32807355 0.0652303 40 M00271 (AML-1a) M00273 (R) M00722 (core-binding factor) M00731 (Osf2) M00751 (AML1) M00769 (AML) 0.7926008 0.17726 41 M00021 (Kr) M00048 (ADR1) M00446 (Spz1) M00633 (GBF) 0.222845033333333 0.0676524 42 M00127 (GATA-1) M00346 (GATA-1) M00347 (GATA-1) M00348 (GATA-2) M00349 (GATA-2) M00350 (GATA-3) M00487 (mtTFA) 0.598487 0.292533 43 M00518 (PPARalpha/RXR-alpha) M00631 (FXR) M00647 (LXR) M00766 (LXR direct repeat 4) 0.684422666666667 0.382025 44 M00279 (MIF-1) M00280 (RFX1) M00281 (RFX1) 0.706104 0.559156 45 M00711 (Zta) M00733 (SMAD-4) M00792 (SMAD) 0.209077 0.111464 46 M00701 (SMAD-3) M00733 (SMAD-4) 0.522049 0.522049 47 M00038 (GCN4) M00495 (Bach1) 0.877154 0.877154 48 M00183 (c-Myb) M00345 (GAmyb) M00773 (MYB) 0.401036333333333 0.15245 49 M00132 (HNF-1) M00478 (Cdc5) M00790 (HNF-1) 0.443635333333333 0.369388 50 M00173 (AP-1) M00174 (AP-1) M00188 (AP-1) M00490 (Bach2) M00517 (AP-1) 0.5670777 0.117537 51 M00099 (S8) M00248 (Oct-1) M00416 (Cart-1) M00437 (CHX10) 0.328015833333333 0.148264 52 M00272 (p53) M00761 (p53 decamer) 0.604321 0.604321 53 M00031 (MATalpha2) M00272 (p53) 0.155115 0.155115 54 M00078 (Evi-1) M00079 (Evi-1) M00082 (Evi-1) 0.73043 0.652772 55 M00158 (COUP-TF / HNF-4) M00242 (PPARalpha/RXR-alpha) M00762 (direct repeat 1) 0.808703333333333 0.722824 56 M00086 (Ik-1) M00088 (Ik-3) 0.628371 0.628371 57 M00115 (Tax/CREB) M00179 (CRE-BP1) M00694 (E4F1) 1 1 58 M00389 (FACB) M00630 (FOXM1) 0.633512 0.633512 59 M00042 (Sox-5) M00160 (SRY) M00276 (Mat1-Mc) M00410 (SOX-9) M00728 (ROX1) 0.52674209 0.0888879 60 M00095 (CDP) M00310 (APOLYA) M00318 (Lentiviral Poly A) 0.822180333333333 0.723954 61 M00457 (STAT5A (homodimer)) M00494 (STAT6) 0.22403 0.22403 62 M00457 (STAT5A (homodimer)) M00499 (STAT5A) 0.176778 0.176778 63 M00016 (E74A) M00025 (Elk-1) 0.711459 0.711459 64 M00016 (E74A) M00771 (ETS) 0.0654194 0.0654194 65 M00067 (Hairy) M00139 (AhR) M00235 (AhR/Arnt) M00237 (AhR/Arnt) M00778 (AhR) 0.7681968 0.425243 66 M00392 (AGL3) M00393 (AGL3) 0.606721 0.606721 67 M00133 (Tst-1) M00162 (Oct-1) M00394 (Msx-1) M00395 (HOXA3) 0.5581305 0.380709 68 M00131 (HNF-3beta) M00289 (HFH-3) M00422 (FOXJ2) M00724 (HNF-3alpha) M00791 (HNF-3) M00809 (FOX) 0.408790333333333 0.139114 69 M00231 (MEF-2) M00232 (MEF-2) M00233 (MEF-2) M00266 (Croc) 0.361274833333333 0.25469 70 M00313 (GEN_INI) M00314 (GEN_INI) M00315 (GEN_INI) 1 1 71 M00022 (Hb) M00380 (Pax-4) 0.0959955 0.0959955 72 M00022 (Hb) M00734 (CIZ) 0.218828 0.218828 73 M00102 (CDP) M00103 (Clox) 0.685583 0.685583 74 M00046 (GCR1) M00108 (NRF-2) M00337 (GCR1) M00531 (NERF1a) M00655 (PEA3) M00658 (PU.1) M00743 (c-Ets-1 68) M00746 (ELF-1) 0.680880785714285 0.244441 75 M00092 (BR-C Z2) M00186 (SRF) M00810 (SRF) 0.413918333333333 0.191348 76 M00396 (En-1) M00622 (C/EBPgamma) M00704 (TEF-1) 0.2711 0.187992 77 M00444 (VDR) M00448 (Zic1) M00449 (Zic2) M00720 (CAC-binding protein) 0.459733666666667 0.265679 78 M00144 (BSAP) M00730 (HAC1) 0.733359 0.733359 79 M00056 (myogenin / NF-1) M00193 (NF-1) M00806 (NF-1) 0.371932 0.279833 80 M00024 (E2F) M00062 (IRF-1) M00063 (IRF-2) M00120 (dl) 0.718624833333333 0.302779 81 M00763 (PPAR direct repeat 1) M00765 (COUP direct repeat 1) 0.677514 0.677514 82 M00029 (HSF) M00146 (HSF1) M00167 (HSF) M00168 (HSF) 0.7500365 0.500073 83 M00009 (Ttk 69K) M00032 (c-Ets-1(p54)) M00074 (c-Ets-1(p54)) M00306 (LEU3) 0.37653795 0.0832207 84 M00084 (MZF1) M00154 (STRE) M00308 (STRE) 0.518568333333333 0.138862 85 M00230 (Skn-1) M00417 (ATHB-9) 1 1 86 M00028 (HSF) M00163 (HSF) M00164 (HSF) 1 1 87 M00189 (AP-2) M00470 (AP-2gamma) 0.0901327 0.0901327 88 M00469 (AP-2alpha) M00470 (AP-2gamma) 0.323709 0.323709 89 M00274 (STE11) M00362 (dTCF) M00411 (HNF-4alpha1) M00805 (LEF1) 0.728197833333333 0.353478 90 M00476 (FOXO4) M00477 (FOXO3) M00742 (HFH-4) 0.747334666666667 0.557889 91 M00089 (Athb-1) M00503 (ATHB-5) 0.453189 0.453189 92 M00026 (RSRFC4) M00407 (RSRFC4) 0.850827 0.850827 93 M00187 (USF) M00322 (c-Myc/Max) 0.081123 0.081123 94 M00040 (CRE-BP1) M00398 (ces-2) 0.0961279 0.0961279 95 M00075 (GATA-1) M00076 (GATA-2) M00077 (GATA-3) 0.234258333333333 0.110291 96 M00012 (CF2-II) M00013 (CF2-II) 0.963327 0.963327 97 M00124 (Pbx1b) M00639 (HNF-6) 1 1 98 M00192 (GR) M00447 (AR) M00481 (AR) 0.513128333333333 0.247114 99 M00316 (Imperfect Hogness/Goldberg BOX) M00352 (Dof1) M00355 (PBF) 0.3909262 0.0967056 100 M00438 (ARF) M00456 (FAC1) 0.0812498 0.0812498 101 M00044 (Sn) M00438 (ARF) 0.0728459 0.0728459 102 M00438 (ARF) M00759 (MCM1+SFF) 0.202559 0.202559 103 M00439 (C1) M00506 (LIM1) M00706 (TFII-I) 0.281791 0.174898 104 M00007 (Elk-1) M00648 (MAF) M00678 (Tel-2) 0.900188666666667 0.850283 105 M00460 (STAT5A (homotetramer)) M00493 (STAT5A) 0.710955 0.710955 106 M00240 (Nkx2-5) M00747 (IRF1) 0.408982 0.408982 107 M00240 (Nkx2-5) M00468 (AP-2rep) 0.21086 0.21086 108 M00001 (MyoD) M00002 (E47) M00071 (E47) M00412 (AREB6) M00414 (AREB6) M00693 (E12) 0.7623964 0.569511 109 M00184 (MyoD) M00277 (Lmo2 complex) M00712 (myogenin) M00804 (E2A) 0.710796333333333 0.523079 110 M00020 (Ftz) M00424 (NKX6-1) M00510 (Lhx3) 1 1 111 M00321 (Muscle initiator) M00378 (Pax-4) M00467 (Roaz) M00776 (SREBP) 0.423789 0.108403 112 M00122 (USF) M00123 (c-Myc/Max) M00220 (SREBP-1) M00796 (USF) 0.216732333333333 0.104806 113 M00443 (Opaque2) M00513 (ATF3) M00514 (ATF4) M00691 (ATF-1) 0.486512666666667 0.14284 114 M00634 (GCM) M00666 (Sry-beta) 1 1 115 M00258 (ISRE) M00415 (AREB6) M00699 (ICSBP) 0.588213666666667 0.431198 116 M00450 (Zic3) M00721 (CACCC-binding factor) M00753 (RCS1) 0.843344333333333 0.716629 117 M00051 (NF-kappaB (p50)) M00083 (MZF1) M00261 (Olf-1) 0.426828 0.270218 118 M00507 (TRAB1) M00654 (OSBZ8) M00726 (USF2) 0.816787 0.711095 119 M00328 (Pax-8) M00373 (Pax-4) M00717 (Pax-8) 0.430994 0.125778 120 M00218 (MYB.Ph3) M00326 (Pax-1) 0.74393 0.74393 121 M00003 (v-Myb) M00227 (v-Myb) M00326 (Pax-1) 0.773976 0.410074 122 M00005 (AP-4) M00175 (AP-4) M00176 (AP-4) M00644 (LBP-1) M00698 (HEB) 0.931802 0.826929 123 M00065 (Tal-1beta/E47) M00066 (Tal-1alpha/E47) M00070 (Tal-1beta/ITF-2) M00532 (RP58) 0.803442 0.733469 124 M00165 (HSF) M00166 (HSF) 1 1 125 M00112 (CF1 / USP) M00156 (RORalpha1) M00157 (RORalpha2) M00239 (v-ErbA) 0.957251333333333 0.868283 126 M00011 (Evi-1) M00080 (Evi-1) 1 1 127 M00238 (Barbie Box) M00353 (Dof2) M00354 (Dof3) 0.901881333333333 0.858886 128 M00290 (Freac-2) M00292 (Freac-4) M00294 (HFH-8) M00474 (FOXO1) M00475 (DAF-16) 0.6927188 0.303962 129 M00045 (E4BP4) M00228 (VBP) M00464 (POU3F2) 0.387619333333333 0.275692 130 M00736 (E2F-1/DP-1) M00737 (E2F-1/DP-2) M00739 (E2F-4/DP-2) 0.793314666666667 0.687357 131 M00727 (SF-1) M00754 (ZAP1) 0.511834 0.511834 132 M00117 (C/EBPbeta) M00690 (AP-3) 0.433551 0.433551 133 M00100 (CdxA) M00690 (AP-3) 0.117474 0.117474 134 M00111 (CF1 / USP) M00191 (ER) M00511 (ERR alpha) M00515 (PPARG) 0.3606515 0.262264 135 M00155 (ARP-1) M00646 (LF-A1) 0.925378 0.925378 136 M00059 (YY1) M00069 (YY1) M00651 (NF-muE1) M00793 (YY1) 0.572766166666667 0.190376 137 M00126 (GATA-1) M00128 (GATA-1) M00142 (NIT2) M00278 (Lmo2 complex) 0.728798166666667 0.258298 138 M00107 (E2) M00181 (E2) 0.613446 0.613446 139 M00149 (SBF-1) M00423 (FOXJ2) M00616 (AFP1) 0.465218 0.269549 140 M00229 (Skn-1) M00284 (TCF11/MafG) M00285 (TCF11) 0.506899666666667 0.270708 141 M00058 (HEN1) M00068 (HEN1) 0.401413 0.401413 142 M00018 (Ubx) M00023 (Hox-1.3) M00436 (IPF1) 0.900706666666667 0.776352 143 M00050 (E2F) M00425 (E2F) 0.796617 0.796617 144 M00169 (HSF) M00170 (HSF) 1 1 145 M00516 (E2F) M00738 (E2F-4/DP-1) M00740 (Rb/E2F-1/DP-1) M00803 (E2F) 0.547948833333333 0.191929