Anterior Epidermis Anterior Epidermis KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C11.485 Irx-B 1.0982 127.5106 0.9210 342.5323 Yes No PWM Hits No PWM Hits KH2012:KH.C1.159 E(spl)/hairy-a 1.3445 65.6302 0.6908 14.3413 Not Analyzed -15.2125 No PWM Hits KH2012:KH.L39.1 FoxH-b 0.6677 45.8148 1.1074 185.2909 No -3.3335 5.2695 KH2012:KH.C1.99 SoxB1 1.2482 73.2413 0.3331 9.3534 Not Analyzed No PWM match No PWM match KH2012:KH.C1.159 E(spl)/hairy-a 0.6233 47.2239 0.4339 77.0192 Yes -10.496 No PWM Hits KH2012:KH.C11.485 Irx-B 1.2355 72.8859 0.1608 0.0137 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.C7.43 AP-2-like2 0.4991 31.7939 0.4775 68.8091 Yes 10.551 21.586 KH2012:KH.C1.1016 GCNF 0.8556 36.2030 1.3828 100.1236 Not Analyzed No PWM match No PWM match KH2012:KH.C1.99 SoxB1 0.4913 33.7808 0.3406 39.0890 No No PWM match No PWM match KH2012:KH.L108.4 CREB/ATF-a 0.6859 37.8207 0.3453 15.8154 Not Analyzed 6.405 8.6245 KH2012:KH.C7.157 Emc 0.4139 19.2080 1.1001 173.3024 Yes No PWM match No PWM match KH2012:KH.S164.12 SoxB2 0.6194 22.8414 0.6433 35.7335 Not Analyzed 8.722 17.405 KH2012:KH.C4.366 ERF2 -0.4878 -32.3767 -0.1770 -0.2316 No -10.324 9.7885 KH2012:KH.L4.17 (C2H2)-18 0.6166 24.8925 0.2386 5.3130 Not Analyzed 6.466 6.466 KH2012:KH.C7.523 SoxC -0.5820 -52.0996 -0.0577 -1.6313 No No PWM match No PWM match KH2012:KH.C9.580 RAR 0.6152 27.0563 1.0325 86.5965 Not Analyzed 0.052 2.73 KH2012:KH.S816.1 ZicL -0.8903 -52.8775 0.1700 34.3239 No 0.7115 0.7115 KH2012:KH.C7.43 AP-2-like2 0.5953 22.5619 0.2400 3.7211 Not Analyzed 14.057 14.7395 KH2012:KH.C4.84 Otx -1.0785 -109.9402 -0.4594 -13.2370 No 0.467 5.2695 KH2012:KH.L40.18 Zinc Finger (C2H2)-6 0.4706 21.2706 0.4690 32.7866 Not Analyzed -4.0385 -4.0385 KH2012:KH.C4.182 Zinc Finger (C3H) -1.2202 -107.4474 0.3847 102.4425 No No PWM match No PWM match KH2012:KH.C13.22 Zinc Finger (C2H2)-2 0.4169 7.4020 -0.4259 -39.3361 Not Analyzed 2.402 13.445 KH2012:KH.S544.3 DMRT1 -1.2611 -149.5385 -0.0953 -2.7101 No 3.431 9.239 KH2012:KH.S696.1 GATA-b 0.4090 21.6057 0.3420 14.6967 Not Analyzed -0.6295 10.9695 KH2012:KH.C8.247 ELK -2.0829 -170.7374 -0.1305 -2.1574 No -12.681 9.7885 KH2012:KH.C4.182 Zinc Finger (C3H) -0.4272 -24.3495 0.6312 10.6359 Not Analyzed No PWM match No PWM match KH2012:KH.C3.17 ROR -0.4850 -22.7587 0.1128 5.2102 Not Analyzed -0.9015 3.907 KH2012:KH.C10.113 ets/pointed2 -0.5146 -24.2580 -0.3177 -31.9516 Not Analyzed -16.398 3.2915 KH2012:KH.L57.25 FoxC -0.8466 -69.2860 -0.0031 -1.3873 Not Analyzed 9.1995 14.8445 JASPAR 2020 Max Z-score Max Z-score KH2012:KH.C4.366 ERF2 -1.0039 -80.6543 -0.0518 -16.0595 Not Analyzed -10.3965 3.2915 PWM cluster in cluster in cluster KH2012:KH.C3.751 Snail -1.0079 -39.8516 -0.0410 -5.1926 Not Analyzed 4.2905 7.928 KH2012:KH.S544.3 DMRT1 -1.0442 -134.6501 -0.1011 -27.4150 Not Analyzed 4.164 13.155 ZNF143 24.97 ZNF143 KH2012:KH.C7.523 SoxC -1.3135 -125.5026 -0.1220 -20.3646 Not Analyzed No PWM match No PWM match TFAP2B 21.59 Znf423 KH2012:KH.S816.1 ZicL -1.3498 -85.6682 -0.1574 -15.3644 Not Analyzed -10.7945 -3.545 HOXD10 17.53 HOXD12 KH2012:KH.C1.274 MyTF -1.5106 -55.8673 0.0209 0.5970 Not Analyzed -4.696 -3.545 PROX1 17.22 PROX1 KH2012:KH.C8.247 ELK -2.2359 -124.9146 -0.1808 -30.7462 Not Analyzed -11.893 3.2915 NFIL3 16.65 NFIL3 KH2012:KH.C4.84 Otx -2.4870 -191.4256 0.5306 5.2412 Not Analyzed -2.873 -2.8185 SP3 16.06 KLF17 POU3F1 16.05 POU2F2 Nr2f6 15.93 PPARA::RXRA SOX8 15.71 SOX21 JASPAR 2020 Max Z-score Max Z-score E2F7 15.00 PWM cluster in cluster in cluster POU3F1 27.82 POU2F2 FOS::JUNB 19.91 Nfe2l2 SOX8 17.41 Dmrt1 HOXD10 16.58 HOXD11

Column 1/2 Row V/VI KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.L57.25 FoxC 1.5295 29.6151 1.5073 85.1285 Yes 4.6425 6.1785 KH2012:KH.L39.1 FoxH-b 1.2834 24.2401 0.8328 26.4493 No -5.2455 1.699 KH2012:KH.C7.43 AP-2-like2 0.9978 15.9821 0.4928 8.1747 No 14.783 16.695 KH2012:KH.C9.717 FoxH-a 0.8765 14.5761 1.7625 106.3217 No -5.2455 1.699 KH2012:KH.C9.580 RAR 0.7037 9.9925 0.8727 22.4594 No -6.117 -6.117 KH2012:KH.C7.269 Orphan bHLH1 0.6402 6.2447 0.6953 15.0676 No No PWM match No PWM match KH2012:KH.L13.24 FoxN2/3 0.6051 8.0454 0.6094 13.9095 No -1.5555 6.1785 KH2012:KH.C2.573 Smad1/5 0.4702 6.0322 0.2006 2.6512 No No PWM Hits No PWM Hits KH2012:KH.C7.157 Emc 0.4273 3.2627 0.5103 4.0038 No No PWM match No PWM match KH2012:KH.C7.127 polybromo -0.4166 -5.5982 -0.1116 -2.2166 No No PWM match No PWM match KH2012:KH.C4.509 Zinc Finger (absent, small, or homeotic discs 1) -0.4575 -5.8914 -0.1007 -2.4802 No No PWM match No PWM match KH2012:KH.C7.523 SoxC -0.4662 -3.4896 0.5889 8.0527 No No PWM match No PWM match KH2012:KH.C8.419 HMG2-like -0.4690 -4.1905 -0.3330 -8.5911 No No PWM match No PWM match KH2012:KH.C4.366 ERF2 -0.5003 -7.8621 0.2286 1.8496 No -4.441 3.836 KH2012:KH.C3.312 E(spl)/hairy-b -0.5129 -7.5802 -0.1241 -3.8227 No 1.8835 No PWM Hits KH2012:KH.C3.348 E12/E47 -0.6951 -12.4333 0.3471 7.3654 No 1.0625 7.794 KH2012:KH.C4.84 Otx -0.8068 -20.3214 1.4575 59.0542 No 1.699 1.699 KH2012:KH.S816.1 ZicL -1.6768 -33.8459 -0.6886 -16.4627 No -3.6715 -0.067 KH2012:KH.C8.247 ELK -2.2165 -39.0717 -1.5309 -57.5828 No -4.5465 3.836 KH2012:KH.C1.274 MyTF -2.8756 -51.1329 -0.0328 -2.8623 No -4.09 -0.067

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster SP3 24.92 SP2 TFAP2B 16.70 TFAP2E

Column 1/2 Row III/IV KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C1.274 MyTF 2.8756 51.1329 2.8429 88.9503 No No PWM Hits 13.617 KH2012:KH.C8.247 ELK 2.2165 39.0717 0.6856 15.5923 No 5.3045 20.286 KH2012:KH.S816.1 ZicL 1.6768 33.8459 0.9882 21.5203 Yes 5.3655 13.617 KH2012:KH.C4.84 Otx 0.8068 20.3214 2.2643 58.1074 No -1.79 6.696 KH2012:KH.C3.348 E12/E47 0.6951 12.4333 1.0422 29.4671 No -1.13 6.668 KH2012:KH.C3.312 E(spl)/hairy-b 0.5129 7.5802 0.3888 3.6441 No -1.404 No PWM Hits KH2012:KH.C4.366 ERF2 0.5003 7.8621 0.7289 16.5058 No 6.868 20.286 KH2012:KH.C8.419 HMG2-like 0.4690 4.1905 0.1359 0.2223 No No PWM match No PWM match KH2012:KH.C7.523 SoxC 0.4662 3.4896 1.0550 18.6580 No No PWM match No PWM match KH2012:KH.C4.509 Zinc Finger (absent, small, or homeotic discs 1) 0.4575 5.8914 0.3568 4.5181 No No PWM match No PWM match KH2012:KH.C7.127 polybromo 0.4166 5.5982 0.3050 4.8878 No No PWM match No PWM match KH2012:KH.C7.157 Emc -0.4273 -3.2627 0.0830 0.4320 No No PWM match No PWM match KH2012:KH.C2.573 Smad1/5 -0.4702 -6.0322 -0.2697 -4.7371 No No PWM Hits No PWM Hits KH2012:KH.L13.24 FoxN2/3 -0.6051 -8.0454 0.0043 1.0838 No 1.713 5.1045 KH2012:KH.C7.269 Orphan bHLH1 -0.6402 -6.2447 0.0550 0.1055 No No PWM match No PWM match KH2012:KH.C9.580 RAR -0.7037 -9.9925 0.1691 0.5853 No 10.005 10.005 KH2012:KH.C9.717 FoxH-a -0.8765 -14.5761 0.8859 54.0738 No 5.6705 6.696 KH2012:KH.C7.43 AP-2-like2 -0.9978 -15.9821 -0.5050 -11.8621 No -12.4225 2.4 KH2012:KH.L39.1 FoxH-b -1.2834 -24.2401 -0.4506 -6.6449 No 5.6705 6.696 KH2012:KH.L57.25 FoxC -1.5295 -29.6151 -0.0222 -0.9294 No -4.6625 5.1045

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster ELK3 20.29 FLI1 ZNF135 18.34 ZNF135 E2F7 15.35 E2F8

a-neural KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C8.247 ELK 2.0829 170.7374 1.9524 294.1707 No 17.916 36.4495 KH2012:KH.S544.3 DMRT1 1.2611 149.5385 1.1658 292.1890 Yes -2.12 -2.12 KH2012:KH.C4.182 Zinc Finger (C3H) 1.2202 107.4474 1.6049 356.1143 No No PWM match No PWM match KH2012:KH.C4.84 Otx 1.0785 109.9402 0.6191 91.9153 Yes -0.496 5.0925 KH2012:KH.S816.1 ZicL 0.8903 52.8775 1.0602 237.7456 No -0.5815 17.804 KH2012:KH.C7.523 SoxC 0.5820 52.0996 0.5244 94.2202 No No PWM match No PWM match KH2012:KH.C4.366 ERF2 0.4878 32.3767 0.3108 35.2335 No 12.896 36.4495 KH2012:KH.C7.157 Emc -0.4139 -19.2080 0.6862 39.7284 No No PWM match No PWM match KH2012:KH.C1.99 SoxB1 -0.4913 -33.7808 -0.1507 -1.1311 No No PWM match No PWM match KH2012:KH.C7.43 AP-2-like2 -0.4991 -31.7939 -0.0216 -2.7044 No -7.5955 5.4895 KH2012:KH.C1.159 E(spl)/hairy-a -0.6233 -47.2239 -0.1894 -4.3427 No 11.9575 No PWM Hits KH2012:KH.L39.1 FoxH-b -0.6677 -45.8148 0.4397 26.9106 No 3.854 5.0925 KH2012:KH.C11.485 Irx-B -1.0982 -127.5106 -0.1771 -2.8433 No No PWM Hits No PWM Hits

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster ELK3 36.45 FLI1 Esrrg 21.68 ESRRA GLIS2 17.80 GLIS2 MEF2D 16.28 MEF2A Rarg 15.80 Rarg FOS::JUNB 15.14 MAFK Column 3 Row V/VI KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.L39.1 FoxH-b 1.1242 11.1873 0.8024 10.8794 No -4.553 6.704 KH2012:KH.C9.580 RAR 1.0760 11.4079 1.4516 20.0267 No -0.8675 -0.8675 KH2012:KH.C9.717 FoxH-a 0.8240 5.7117 1.2467 61.9336 No -4.553 6.704 KH2012:KH.C1.99 SoxB1 0.7989 4.9035 0.1907 0.3398 No No PWM match No PWM match KH2012:KH.C2.573 Smad1/5 0.7368 6.5337 0.4831 4.8527 No No PWM Hits No PWM Hits KH2012:KH.C14.586 Zinc Finger (BTB/C2H2) 0.6318 3.3539 0.2357 1.1698 No -4.7315 -4.7315 KH2012:KH.C9.561 Zinc Finger (C2H2)-9 0.5832 4.7238 0.6796 18.6533 No -4.0835 -3.476 KH2012:KH.C14.520 Orphan Fox-1 0.4792 11.4862 0.4476 13.9772 No -0.1245 5.8615 KH2012:KH.C14.306 IRF-like 2 0.4353 3.7643 0.0793 0.6624 No No PWM match No PWM match KH2012:KH.C12.343 small Maf -0.4059 -4.1063 -0.2015 -2.6287 No 5.9065 11.0285 KH2012:KH.C7.207 FoxP -0.4316 -4.9461 -0.0441 -1.3512 No -0.1895 5.8615 KH2012:KH.C5.50 Zinc Finger (C2H2)-28 -0.4403 -5.7022 0.3511 6.5608 No No PWM match No PWM match KH2012:KH.C1.661 MAD -0.4691 -3.5405 0.2450 1.1554 No No PWM match No PWM match KH2012:KH.C2.687 VDR-a -0.5329 -4.8768 -0.3757 -4.4723 No No PWM match No PWM match KH2012:KH.C7.523 SoxC -0.5438 -5.0271 -0.2838 -2.8104 No No PWM match No PWM match KH2012:KH.C2.725 Su(H)/RBP-J -0.5887 -7.2818 -0.3659 -6.7620 No No PWM Hits No PWM Hits KH2012:KH.C3.17 ROR -0.6540 -5.8422 -0.1056 -1.8791 No -7.2125 3.519 KH2012:KH.C3.348 E12/E47 -0.8709 -11.0006 0.0091 0.0412 No -1.053 11.7855 KH2012:KH.C3.312 E(spl)/hairy-b -0.9713 -7.2487 0.1234 0.0399 No -7.452 No PWM Hits KH2012:KH.C4.366 ERF2 -1.2219 -13.1157 -0.3624 -3.8131 No -0.4845 1.751 KH2012:KH.C10.113 ets/pointed2 -1.3752 -15.4581 -0.6103 -10.2844 No -8.097 1.751 KH2012:KH.C4.84 Otx -1.8162 -20.1682 0.8073 11.4441 No 6.704 6.704 KH2012:KH.S816.1 ZicL -1.9845 -19.7246 -1.0062 -9.6729 No -3.668 2.646 KH2012:KH.C3.751 Snail -2.5984 -21.0349 0.0213 0.2168 No 0.099 11.7855 KH2012:KH.C8.247 ELK -2.7250 -21.1254 -1.7823 -23.6300 No -2.9905 1.751

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster POU3F1 16.63 POU1F1

Animal cells KH2012 TF common name Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster z-score z-score KH2012:KH.C7.157 Emc 1.4078 307.9242 Yes No PWM match No PWM match KH2012:KH.C13.22 Zinc Finger (C2H2)-2 0.9977 261.3980 Yes 1.6715 11.4475 KH2012:KH.C7.43 AP-2-like2 0.9335 286.6523 Yes 9.5685 21.4685 KH2012:KH.C1.99 SoxB1 0.6504 137.3633 No No PWM match No PWM match KH2012:KH.L39.1 FoxH-b 0.5529 73.0560 No -3.9245 7.4325 KH2012:KH.C11.485 Irx-B -0.3992 -113.4184 No No PWM Hits No PWM Hits KH2012:KH.C1.727 macho-1 -0.4352 -56.6562 No -7.521 No PWM Hits KH2012:KH.C4.84 Otx -0.4461 -47.1821 No 3.9505 7.4325 KH2012:KH.C11.313 FoxA-a -0.4745 -138.6870 No 2.7275 No PWM Hits KH2012:KH.C3.312 E(spl)/hairy-b -0.4968 -170.8977 No -11.4445 No PWM Hits KH2012:KH.S215.4 Lhx3 -0.5425 -135.1856 No 5.9525 8.195 KH2012:KH.C3.751 Snail -0.5623 -175.6120 No 1.116 11.9005 Column 3 Row III/IV KH2012:KH.S816.1 ZicL -0.7187 -274.4453 No -8.092 2.044 KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C8.247 ELK 2.7250 21.1254 0.9428 27.1916 No 4.5535 23.4555 JASPAR 2020 Max Z-score Max Z-score KH2012:KH.C3.751 Snail 2.5984 21.0349 2.6197 89.4868 No 0.0330000000000001 18.1775 PWM cluster in cluster in cluster KH2012:KH.S816.1 ZicL 1.9845 19.7246 0.9782 21.3602 Yes 6.0645 11.4975 RARA_var_2_ 28.64 RARA::RXRG KH2012:KH.C4.84 Otx 1.8162 20.1682 2.6235 46.4537 No -8.75 6.7725 TFAP2B 21.47 TFAP2C KH2012:KH.C10.113 ets/pointed2 1.3752 15.4581 0.7649 21.2432 No 13.5755 23.4555 Stat5a::Stat5b 16.01 Stat6 KH2012:KH.C4.366 ERF2 1.2219 13.1157 0.8595 18.4508 No 0.9 23.4555 ELK3 15.84 ZBTB7A KH2012:KH.C3.312 E(spl)/hairy-b 0.9713 7.2487 1.0947 22.4645 No 11.3625 No PWM Hits Rarg 15.66 NR1D1 KH2012:KH.C3.348 E12/E47 0.8709 11.0006 0.8801 23.3204 No 1.373 18.1775 KH2012:KH.C3.17 ROR 0.6540 5.8422 0.5484 9.7205 No 13.189 25.0885 KH2012:KH.C2.725 Su(H)/RBP-J 0.5887 7.2818 0.2228 2.0833 No No PWM Hits No PWM Hits KH2012:KH.C7.523 SoxC 0.5438 5.0271 0.2601 3.6929 No No PWM match No PWM match KH2012:KH.C2.687 VDR-a 0.5329 4.8768 0.1571 0.9974 No No PWM match No PWM match KH2012:KH.C1.661 MAD 0.4691 3.5405 0.7141 15.4869 No No PWM match No PWM match KH2012:KH.C5.50 Zinc Finger (C2H2)-28 0.4403 5.7022 0.7913 26.0326 No No PWM match No PWM match KH2012:KH.C7.207 FoxP 0.4316 4.9461 0.3875 12.5776 No 0.5495 9.6405 KH2012:KH.C12.343 small Maf 0.4059 4.1063 0.2044 2.3813 No -2.6165 0.9625 KH2012:KH.C14.306 IRF-like 2 -0.4353 -3.7643 -0.3560 -6.7469 No No PWM match No PWM match KH2012:KH.C14.520 Orphan Fox-1 -0.4792 -11.4862 -0.0316 -0.1157 No 0.1535 9.6405 KH2012:KH.C9.561 Zinc Finger (C2H2)-9 -0.5832 -4.7238 0.0964 1.7267 No 8.3875 8.3875 KH2012:KH.C14.586 Zinc Finger (BTB/C2H2) -0.6318 -3.3539 -0.3961 -6.2385 No 7.26 7.26 KH2012:KH.C2.573 Smad1/5 -0.7368 -6.5337 -0.2537 -2.8036 No No PWM Hits No PWM Hits KH2012:KH.C1.99 SoxB1 -0.7989 -4.9035 -0.6082 -10.6892 No No PWM match No PWM match KH2012:KH.C9.717 FoxH-a -0.8240 -5.7117 0.4227 33.9526 No 6.7725 6.7725 KH2012:KH.C9.580 RAR -1.0760 -11.4079 0.3756 8.7420 No 1.0455 9.529 KH2012:KH.L39.1 FoxH-b -1.1242 -11.1873 -0.3218 -2.6839 No 6.7725 6.7725

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster NR3C1 37.45 Ar Esrrg 25.09 ESRRB Wt1 24.45 ZNF263 ELK3 23.46 FLI1 ZBED1 21.29 ZBTB33 NR1I2 19.30 NR1I2 ZNF274 19.01 ZNF274 PRDM1 18.82 PRDM1 BHLHA15_var_2_ 18.18 OLIG2 SP3 16.85 SP2 TBX21 16.09 EOMES FOSL2::JUNB_var_2_ 16.09 CREM ARNT2 15.40 USF2

Posterior Epidermis KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.L142.14 Emx 1.1311 37.3289 1.1770 100.7330 Not Analyzed 4.236 10.391 KH2012:KH.C11.485 Irx-B 0.6978 20.0078 0.6291 24.4053 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.C9.580 RAR 0.5393 14.5018 0.9706 76.9492 Not Analyzed -0.862 12.614 KH2012:KH.L39.1 FoxH-b 0.5225 15.5683 0.1459 3.4757 Not Analyzed 0.456 0.456 KH2012:KH.C1.159 E(spl)/hairy-a 0.4679 10.1911 0.8896 55.4508 Not Analyzed -10.114 No PWM Hits KH2012:KH.L13.24 FoxN2/3 0.4489 14.8730 0.8131 99.7123 Not Analyzed 2.882 14.4115 KH2012:KH.S816.1 ZicL -0.6066 -25.7850 -0.0736 -9.7364 Not Analyzed -5.4725 14.4335 KH2012:KH.C3.312 E(spl)/hairy-b -0.6523 -9.1620 0.3269 2.6360 Not Analyzed -10.114 No PWM Hits KH2012:KH.L8.11 Tbx6a -0.6707 -48.9718 -0.0810 -11.1547 Not Analyzed No PWM match No PWM match KH2012:KH.C7.472 Hox12 -1.0344 -65.5464 0.0917 6.8612 Not Analyzed No PWM match No PWM match KH2012:KH.C8.247 ELK -2.2468 -141.7418 -0.3289 -33.0006 Not Analyzed -11.5475 -1.01 KH2012:KH.C6.129 Neurogenin -2.5229 -96.9179 0.0115 6.2198 Not Analyzed -3.797 No PWM Hits

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster ZSCAN4 25.32 ZSCAN4 POU3F1 18.72 POU3F3 Posterior Epidermis KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C13.22 Zinc Finger (C2H2)-2 0.8244 62.1982 0.6479 118.5495 No 0.533 7.602 KH2012:KH.L39.1 FoxH-b 0.7955 50.0431 1.0257 209.0790 No -0.577 1.3515 KH2012:KH.C7.43 AP-2-like2 0.6452 41.4337 0.6983 139.0314 Yes -3.003 37.226 KH2012:KH.C1.159 E(spl)/hairy-a 0.5883 32.0103 0.5511 142.5416 No -16.698 No PWM Hits KH2012:KH.C7.269 Orphan bHLH1 0.4394 27.9780 0.2027 53.7997 No No PWM match No PWM match KH2012:KH.C14.520 Orphan Fox-1 0.4261 45.0651 0.5490 161.5737 No 5.593 9.5955 KH2012:KH.C3.230 Smad6/7 -0.4823 -31.9078 0.1373 41.8025 No No PWM match No PWM match KH2012:KH.C4.366 ERF2 -0.6681 -46.9599 0.0055 9.5802 No -9.236 0.295 KH2012:KH.C7.157 Emc -0.7171 -15.4195 0.3829 32.4283 No No PWM match No PWM match KH2012:KH.S816.1 ZicL -0.7903 -76.2792 -0.0993 -1.3596 No -6.37 5.396 KH2012:KH.C11.485 Irx-B -1.0114 -71.9066 0.2009 71.5288 No No PWM Hits No PWM Hits KH2012:KH.C4.84 Otx -1.1350 -132.7340 -0.4690 -19.3303 No -4.6135 1.3515 KH2012:KH.C8.247 ELK -1.5734 -111.7593 -0.0229 -1.0007 No -13.1525 0.295 KH2012:KH.C2.957 msxb -1.8930 -202.1480 0.0897 8.1420 No 4.6555 8.126

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster TFAP2B 37.23 Znf423 POU3F1 28.65 POU2F3 SOX8 20.75 Dmrt1 ZNF143 16.79 ZNF143 Ventral midline tail epidermis? KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C6.129 Neurogenin 2.5229 96.9179 2.5344 71.0743 Not Analyzed 4.7415 No PWM Hits KH2012:KH.C8.247 ELK 2.2468 141.7418 1.9179 81.8522 Not Analyzed 18.4735 22.866 KH2012:KH.C7.472 Hox12 1.0344 65.5464 1.1261 91.2128 Not Analyzed No PWM match No PWM match KH2012:KH.L8.11 Tbx6a 0.6707 48.9718 0.5897 19.9253 Not Analyzed No PWM match No PWM match KH2012:KH.C3.312 E(spl)/hairy-b 0.6523 9.1620 0.9792 15.2800 Not Analyzed 14.0645 No PWM Hits KH2012:KH.S816.1 ZicL 0.6066 25.7850 0.5330 6.6780 Not Analyzed 9.219 9.957 KH2012:KH.L13.24 FoxN2/3 -0.4489 -14.8730 0.3642 8.0891 Not Analyzed -2.896 1.6535 KH2012:KH.C1.159 E(spl)/hairy-a -0.4679 -10.1911 0.4217 2.6481 Not Analyzed 14.0645 No PWM Hits KH2012:KH.L39.1 FoxH-b -0.5225 -15.5683 -0.3766 -12.9673 Not Analyzed -0.2575 10.996 KH2012:KH.C9.580 RAR -0.5393 -14.5018 0.4313 3.2473 Not Analyzed 0.741 0.741 KH2012:KH.C11.485 Irx-B -0.6978 -20.0078 -0.0687 -6.1890 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.L142.14 Emx -1.1311 -37.3289 0.0460 0.4237 Not Analyzed -4.311 4.997

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster ELK3 22.87 ELK3 RFX2 21.26 RFX5 FOSL2::JUNB_var_2_ 20.00 ATF7 PRDM1 19.57 PRDM1 TP73 19.40 TP53 ARNT2 17.80 FOS::JUNB 17.69 MAFA Esrrg 17.48 ESRRA SP3 17.07 KLF11 SRF 15.81 SRF BHLHA15_var_2_ 15.24 MXI1 Nr2f6 15.09 TCF7

Dorsal midline tail epidermis KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C7.157 Emc 1.6086 33.9890 1.3573 41.9703 Not Analyzed No PWM match No PWM match KH2012:KH.L39.1 FoxH-b 1.3039 25.9244 1.0820 31.4121 Not Analyzed 2.738 2.738 KH2012:KH.C1.1016 GCNF 0.8703 10.1663 1.1605 24.7063 Not Analyzed No PWM match No PWM match KH2012:KH.C7.269 Orphan bHLH1 0.8335 12.8785 0.7835 16.9971 Not Analyzed No PWM match No PWM match KH2012:KH.C9.580 RAR 0.6674 9.4947 1.0513 27.9206 Not Analyzed -2.904 -2.904 KH2012:KH.L4.17 Zinc Finger (C2H2)-18 0.6640 8.1888 0.3998 4.6637 Not Analyzed -1.007 -1.007 KH2012:KH.C7.43 AP-2-like2 0.6452 8.2474 0.2410 1.5155 Not Analyzed 7.195 8.925 KH2012:KH.C2.573 Smad1/5 0.6375 8.3650 -0.1204 -1.8729 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.C11.485 Irx-B 0.6262 7.5401 -0.4884 -11.6674 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.C9.717 FoxH-a 0.5159 7.8019 0.5806 20.2737 Not Analyzed 2.738 2.738 KH2012:KH.C7.782 POU-like 0.4973 6.4575 0.1023 0.9654 Not Analyzed No PWM match No PWM match KH2012:KH.C14.178 HMG1/2 0.4850 16.2854 0.7390 40.5629 Not Analyzed No PWM match No PWM match KH2012:KH.L108.4 CREB/ATF-a 0.4652 6.7459 0.3586 6.5038 Not Analyzed 10.7295 12.2505 KH2012:KH.C9.561 Zinc Finger (C2H2)-9 0.4224 4.3060 0.6757 14.8069 Not Analyzed 0.4445 0.4445 KH2012:KH.C2.957 msxb -0.5201 -12.2833 1.5967 55.6046 Not Analyzed 8.507 11.624 KH2012:KH.C14.408 -0.5438 -12.9454 0.1296 5.4285 Not Analyzed 11.002 17.325 KH2012:KH.C3.17 ROR -0.6306 -9.0362 0.1280 0.1637 Not Analyzed 3.3335 14.8375 KH2012:KH.C14.307 MyoD -0.7214 -25.0884 -0.0134 -1.3281 Not Analyzed -6.888 No PWM Hits KH2012:KH.S816.1 ZicL -1.7397 -48.0614 -0.8300 -27.6078 Not Analyzed -10.114 -1.3175 KH2012:KH.C8.247 ELK -2.5352 -52.4929 -1.4776 -46.4106 Not Analyzed -9.882 4.9915 KH2012:KH.C3.751 Snail -2.6478 -58.9675 0.0949 2.5148 Not Analyzed 1.844 6.902

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster E2F7 23.91 E2F2 POU3F1 20.93 POU2F1 HOXD10 17.33 HOXD9 NFIL3 15.40 NFIL3 b-neural KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C2.957 msxb 1.8930 202.1480 1.9827 623.2395 Yes -4.0795 5.8485 KH2012:KH.C8.247 ELK 1.5734 111.7593 1.5505 160.5299 No 22.4905 22.4905 KH2012:KH.C4.84 Otx 1.1350 132.7340 0.6661 85.4570 No 3.7235 10.7595 KH2012:KH.C11.485 Irx-B 1.0114 71.9066 1.2123 239.9952 No No PWM Hits No PWM Hits KH2012:KH.S816.1 ZicL 0.7903 76.2792 0.6910 125.5040 No 9.258 17.871 KH2012:KH.C7.157 Emc 0.7171 15.4195 1.1000 45.7885 No No PWM match No PWM match KH2012:KH.C4.366 ERF2 0.6681 46.9599 0.6736 69.0654 No 13.0735 22.4905 KH2012:KH.C3.230 Smad6/7 0.4823 31.9078 0.6196 122.3619 No No PWM match No PWM match KH2012:KH.C14.520 Orphan Fox-1 -0.4261 -45.0651 0.1229 4.2451 No -4.882 3.7855 KH2012:KH.C7.269 Orphan bHLH1 -0.4394 -27.9780 -0.2367 -4.2104 No No PWM match No PWM match KH2012:KH.C1.159 E(spl)/hairy-a -0.5883 -32.0103 -0.0372 -2.5675 No 19.1895 No PWM Hits KH2012:KH.C7.43 AP-2-like2 -0.6452 -41.4337 0.0530 5.8665 No 2.5925 12.636 KH2012:KH.L39.1 FoxH-b -0.7955 -50.0431 0.2302 8.5390 No 0.3285 10.7595 KH2012:KH.C13.22 Zinc Finger (C2H2)-2 -0.8244 -62.1982 -0.1766 -1.0971 No -0.55 11.101

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster BHLHA15_var_2_ 23.57 PKNOX2 Esrrg 23.39 ESRRA ELK3 22.49 ELK1 ZNF135 20.72 ZNF135 ZBED1 19.87 ZBTB33 ARNT2 18.43 HES1 GLIS2 17.87 ZIC1

b-neural KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C3.751 Snail 2.6478 58.9675 2.7427 85.2774 No -1.2465 12.049 KH2012:KH.C8.247 ELK 2.5352 52.4929 1.0576 32.3170 No 16.3345 26.116 KH2012:KH.S816.1 ZicL 1.7397 48.0614 0.9097 18.6329 Yes 20.2145 24.193 KH2012:KH.C14.307 MyoD 0.7214 25.0884 0.7080 33.5917 No 9.238 No PWM Hits KH2012:KH.C3.17 ROR 0.6306 9.0362 0.7586 11.9800 No -3.7835 8.9345 KH2012:KH.C14.408 Cdx 0.5438 12.9454 0.6734 31.1064 No -12.025 -1.4185 KH2012:KH.C9.616 Lmx 0.5374 14.9612 0.5374 22.3831 No -10.9245 4.32 KH2012:KH.C2.957 msxb 0.5201 12.2833 2.1168 58.8082 Yes -9.55 4.32 KH2012:KH.C9.561 Zinc Finger (C2H2)-9 -0.4224 -4.3060 0.2533 3.0242 No -0.5895 3.4595 KH2012:KH.L108.4 CREB/ATF-a -0.4652 -6.7459 -0.1066 -1.9034 No -7.764 7.876 KH2012:KH.C14.178 HMG1/2 -0.4850 -16.2854 0.2540 6.5454 No No PWM match No PWM match KH2012:KH.C7.782 POU-like -0.4973 -6.4575 -0.3950 -6.5642 No No PWM match No PWM match KH2012:KH.C9.717 FoxH-a -0.5159 -7.8019 0.0648 1.9903 No -3.2385 8.5645 KH2012:KH.C11.485 Irx-B -0.6262 -7.5401 -1.1146 -32.0137 No No PWM Hits No PWM Hits KH2012:KH.C2.573 Smad1/5 -0.6375 -8.3650 -0.7579 -18.9414 No No PWM Hits No PWM Hits KH2012:KH.C7.43 AP-2-like2 -0.6452 -8.2474 -0.4042 -9.1820 No -7.71 7.935 KH2012:KH.L4.17 Zinc Finger (C2H2)-18 -0.6640 -8.1888 -0.2642 -3.2437 No 1.119 1.119 KH2012:KH.C9.580 RAR -0.6674 -9.4947 0.3840 2.5090 No 3.039 12.525 KH2012:KH.C7.269 Orphan bHLH1 -0.8335 -12.8785 -0.0500 -1.6010 No No PWM match No PWM match KH2012:KH.C1.1016 GCNF -0.8703 -10.1663 0.2901 2.5384 No No PWM match No PWM match KH2012:KH.L39.1 FoxH-b -1.3039 -25.9244 -0.2218 -2.6821 No -3.2385 8.5645 KH2012:KH.C7.157 Emc -1.6086 -33.9890 -0.2513 -1.8557 No No PWM match No PWM match

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster ZNF135 28.20 ZNF135 ELK3 26.12 FLI1 GLIS2 24.19 ZIC5 OVOL2 17.55 MYBL2 ESR1 16.57 ESR2 PAX1 15.34 PAX1 PRDM1 15.32 PRDM1 MAFG 15.09 MAFG

A7.6 A7.6 TLC KH2012 TF common name Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C1.1116 NoTrlc 0.9826 32.8012 Yes No PWM match No PWM match KH2012:KH.C1.1116 NoTrlc 1.2761 19.0227 0.8414 18.4215 Yes No PWM match No PWM match KH2012:KH.C1.274 MyTF 2.0133 51.9607 1.2768 13.2541 Not Analyzed -4.107 5.108 KH2012:KH.C11.485 Irx-B 0.7026 19.4302 No No PWM Hits No PWM Hits KH2012:KH.C1.274 MyTF 0.9956 14.8390 0.7041 15.7828 No 4.548 4.548 KH2012:KH.C5.416 TWIST-like-1a/b 1.5351 52.8428 1.3551 16.9310 Not Analyzed No PWM match No PWM match KH2012:KH.C4.341 FoxB 0.5773 20.9838 Yes 1.043 7.3765 KH2012:KH.C1.99 SoxB1 0.8304 13.6480 0.2546 3.6782 Yes No PWM match No PWM match KH2012:KH.C4.366 ERF2 1.3227 40.2598 0.6245 11.4461 Not Analyzed -3.0165 7.9675 KH2012:KH.L39.1 FoxH-b 0.4548 8.3410 Yes -5.288 2.2015 KH2012:KH.C4.341 FoxB 0.7612 12.9471 0.0454 1.0139 Yes -0.495 4.399 KH2012:KH.C4.84 Otx 1.2664 43.5912 0.8838 22.3213 Not Analyzed -4.199 4.1185 KH2012:KH.C4.182 Zinc Finger (C3H) -0.4588 -8.0409 No No PWM match No PWM match KH2012:KH.L39.1 FoxH-b 0.7438 9.2889 0.2468 4.4362 Yes -1.164 3.9325 KH2012:KH.C1.99 SoxB1 0.7908 21.2716 -0.0242 -2.1467 Not Analyzed No PWM match No PWM match KH2012:KH.C1.159 E(spl)/hairy-a -0.5084 -6.5697 No 3.537 No PWM Hits KH2012:KH.C4.366 ERF2 0.5869 7.4098 0.6307 13.7616 No -6.9215 -1.42 KH2012:KH.C4.539 Fli/ERG1 0.7070 43.3586 0.6702 18.5183 Not Analyzed -3.356 7.9675 KH2012:KH.C11.313 FoxA-a -0.5827 -10.6937 No 4.079 No PWM Hits KH2012:KH.C11.485 Irx-B 0.5579 8.4805 -0.1293 -0.0412 No No PWM Hits No PWM Hits KH2012:KH.C3.312 E(spl)/hairy-b 0.6512 14.1719 0.4267 5.9354 Not Analyzed 10.906 No PWM Hits KH2012:KH.C3.312 E(spl)/hairy-b -0.6055 -12.3513 No 3.537 No PWM Hits KH2012:KH.C7.157 Emc 0.5367 6.3888 0.9691 24.5271 No No PWM match No PWM match KH2012:KH.L96.11 Groucho2 0.6026 15.8830 0.0511 0.5638 Not Analyzed No PWM match No PWM match KH2012:KH.C8.247 ELK -0.8938 -17.1147 No -5.5355 1.235 KH2012:KH.C14.520 Orphan Fox-1 0.4925 12.3280 0.2376 6.6144 No 0.71 4.399 KH2012:KH.C5.202 TWIST-like-2 0.5950 24.2922 0.5869 9.8728 Not Analyzed No PWM match No PWM match KH2012:KH.S215.4 Lhx3 -1.0191 -23.2223 No -1.907 10.8005 KH2012:KH.C14.105 CNOT7/8 0.4540 4.6582 -0.1212 -2.2587 No No PWM match No PWM match KH2012:KH.L39.1 FoxH-b 0.5572 11.7482 -0.1987 -3.2954 Not Analyzed -0.7605 4.1185 KH2012:KH.C6.129 Neurogenin 0.4490 4.0000 0.2687 5.5848 No 5.488 No PWM Hits KH2012:KH.C14.520 Orphan Fox-1 0.4884 17.9795 -0.1619 -2.8076 Not Analyzed -3.2075 3.945

KH2012:KH.C2.687 VDR-a -0.4169 -7.6383 -0.2072 -1.8099 No No PWM match No PWM match KH2012:KH.C11.485 Irx-B 0.4572 13.5345 0.1000 0.7249 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.C3.230 Smad6/7 -0.5015 -12.6583 0.0815 1.4505 No No PWM match No PWM match KH2012:KH.C4.182 Zinc Finger (C3H) -0.4069 -8.6690 2.2055 39.2700 Not Analyzed No PWM match No PWM match JASPAR 2020 Max Z-score Max Z-score KH2012:KH.L4.17 Zinc Finger (C2H2)-18 -0.6422 -8.7160 0.3750 2.8370 No -6.986 -6.986 KH2012:KH.L4.17 Zinc Finger (C2H2)-18 -0.5911 -15.0580 0.8567 14.3849 Not Analyzed -3.476 -3.476 PWM cluster in cluster in cluster KH2012:KH.C11.313 FoxA-a -0.7352 -16.2011 -0.1371 -0.7658 No -3.766 No PWM Hits KH2012:KH.C1.159 E(spl)/hairy-a -0.7461 -13.1510 0.1852 0.4051 Not Analyzed 10.906 No PWM Hits KH2012:KH.C4.84 Otx -0.8239 -13.1569 1.1745 28.2914 No -3.6105 3.9325 SP3 16.52 EGR1 KH2012:KH.C10.338 TTF1 -1.2186 -37.6866 0.0047 1.2908 No No PWM Hits No PWM Hits FOS::JUNB 15.93 MAF::NFE2 KH2012:KH.C4.182 Zinc Finger (C3H) -1.2577 -13.7084 0.2957 8.0139 No No PWM match No PWM match KH2012:KH.S215.4 Lhx3 -1.6905 -39.6698 -0.2676 -4.1159 No -5.876 14.4915 JASPAR 2020 Max Z-score Max Z-score KH2012:KH.C8.247 ELK -2.2108 -30.3247 0.5229 7.7418 No -8.0715 -1.42 PWM cluster in cluster in cluster ARNT2 25.55 MYC ZNF143 22.12 ZNF143 BHLHA15_var_2_ 20.79 MXI1 JASPAR 2020 Max Z-score Max Z-score FOSL2::JUNB_var_2_ 17.77 CREM PWM cluster in cluster in cluster INSM1 17.16 INSM1 Esrrg 28.35 NR2F1 E2F7 15.99 E2F2 FOSL2::JUNB_var_2_ 19.40 ATF7 SOX8 15.99 SOX4 TEAD4 16.99 TEAD2 TBX21 15.41 TBX2

Anterior Endoderm KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C1.1116 NoTrlc 2.4188 46.8305 1.9067 23.1954 Not Analyzed No PWM match No PWM match KH2012:KH.L24.23 Myc 0.5105 4.9445 0.2948 0.6130 Not Analyzed 1.1495 No PWM Hits KH2012:KH.C7.157 Emc 0.4789 4.1402 2.0283 21.0873 Not Analyzed No PWM match No PWM match KH2012:KH.C4.366 ERF2 0.4525 4.0588 0.0365 0.3576 Not Analyzed -1.8055 14.162 KH2012:KH.C14.448 AP4 0.4246 3.7738 0.4745 2.4462 Not Analyzed 5.755 23.103 KH2012:KH.C4.182 Zinc Finger (C3H) 0.4153 7.9563 1.4915 22.3872 Not Analyzed No PWM match No PWM match KH2012:KH.C1.274 MyTF 0.4065 6.2389 0.3931 2.2414 Not Analyzed -4.254 2.7155 KH2012:KH.S899.4 BTF3 -0.4041 -7.6627 0.0796 0.7578 Not Analyzed No PWM match No PWM match KH2012:KH.C10.367 Six36 -0.4050 -10.5325 0.0439 1.0254 Not Analyzed 5.389 5.389 KH2012:KH.C8.396 FoxD-a/b -0.8205 -16.5075 -0.0774 -6.5533 Not Analyzed -0.6155 6.467

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster PBX3 23.10 PKNOX1 Endoderm Endoderm BHLHA15_var_2_ 23.10 TGIF2 KH2012 TF common name Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.S215.4 Lhx3 1.0191 23.2223 Yes 3.1445 12.508 KH2012:KH.C8.247 ELK 2.2108 30.3247 1.8399 32.7473 Yes 12.7335 38.0495 KH2012:KH.C8.247 ELK 0.8938 17.1147 Yes 13.964 33.234 KH2012:KH.S215.4 Lhx3 1.6905 39.6698 0.4038 7.1695 Yes 10.0975 10.0975 KH2012:KH.C3.312 E(spl)/hairy-b 0.6055 12.3513 No -4.3555 No PWM Hits KH2012:KH.C4.182 Zinc Finger (C3H) 1.2577 13.7084 1.0946 14.8853 Yes No PWM match No PWM match KH2012:KH.C11.313 FoxA-a 0.5827 10.6937 Yes -6.389 No PWM Hits KH2012:KH.C10.338 TTF1 1.2186 37.6866 0.8668 23.5331 No No PWM Hits No PWM Hits KH2012:KH.C1.159 E(spl)/hairy-a 0.5084 6.5697 No -4.3555 No PWM Hits KH2012:KH.C4.84 Otx 0.8239 13.1569 1.7504 33.6220 No 3.879 9.809 KH2012:KH.C4.182 Zinc Finger (C3H) 0.4588 8.0409 Yes No PWM match No PWM match KH2012:KH.C11.313 FoxA-a 0.7352 16.2011 0.0154 1.0375 Yes 4.9445 No PWM Hits KH2012:KH.L39.1 FoxH-b -0.4548 -8.3410 No 9.614 9.614 KH2012:KH.L4.17 Zinc Finger (C2H2)-18 0.6422 8.7160 0.6854 9.3902 No 11.276 11.276 KH2012:KH.C4.341 FoxB -0.5773 -20.9838 No -1.8835 9.1935 KH2012:KH.C3.230 Smad6/7 0.5015 12.6583 0.5924 25.2582 No No PWM match No PWM match KH2012:KH.C11.485 Irx-B -0.7026 -19.4302 No No PWM Hits No PWM Hits KH2012:KH.C2.687 VDR-a 0.4169 7.6383 -0.0081 -0.6288 No No PWM match No PWM match KH2012:KH.C1.1116 NoTrlc -0.9826 -32.8012 No No PWM match No PWM match KH2012:KH.C6.129 Neurogenin -0.4490 -4.0000 -0.1870 -0.2688 No -5.841 No PWM Hits KH2012:KH.C14.105 CNOT7/8 -0.4540 -4.6582 -0.5201 -7.1966 No No PWM match No PWM match KH2012:KH.C14.520 Orphan Fox-1 -0.4925 -12.3280 -0.1737 -2.8359 No -0.5385 7.288 KH2012:KH.C7.157 Emc -0.5367 -6.3888 0.7445 19.4444 No No PWM match No PWM match JASPAR 2020 Max Z-score Max Z-score KH2012:KH.C11.485 Irx-B -0.5579 -8.4805 0.0154 0.5850 No No PWM Hits No PWM Hits PWM cluster in cluster in cluster KH2012:KH.C4.366 ERF2 -0.5869 -7.4098 0.0336 0.4442 No 10.008 38.0495 KH2012:KH.L39.1 FoxH-b -0.7438 -9.2889 -0.0422 -2.0494 No 1.395 9.809 ELK3 33.23 ELF1 KH2012:KH.C4.341 FoxB -0.7612 -12.9471 -0.1385 -1.7723 No 0.9345 7.288 RARA_var_2_ 25.03 RARA::RXRG KH2012:KH.C1.99 SoxB1 -0.8304 -13.6480 -0.5234 -3.4703 No No PWM match No PWM match TP73 20.05 TP73 KH2012:KH.C1.274 MyTF -0.9956 -14.8390 -0.0558 -0.6377 No -3.393 12.084 Posterior Endoderm NR3C1 19.62 NR3C1 KH2012:KH.C1.1116 NoTrlc -1.2761 -19.0227 0.5478 10.7099 No No PWM match No PWM match SP3 15.46 KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score

KH2012:KH.C8.396 FoxD-a/b 0.8205 16.5075 0.7432 2.4212 Not Analyzed 0.615 7.0325 JASPAR 2020 Max Z-score Max Z-score KH2012:KH.C10.367 Six36 0.4050 10.5325 0.4488 5.4100 Not Analyzed -4.166 0.2215 PWM cluster in cluster in cluster KH2012:KH.S899.4 BTF3 0.4041 7.6627 0.4837 8.1157 Not Analyzed No PWM match No PWM match KH2012:KH.C1.274 MyTF -0.4065 -6.2389 -0.0134 -1.4644 Not Analyzed No PWM Hits 20.13 ELK3 38.05 ETV1 KH2012:KH.C4.182 Zinc Finger (C3H) -0.4153 -7.9563 1.0761 12.7787 Not Analyzed No PWM match No PWM match ZNF135 27.75 ZNF135 KH2012:KH.C14.448 AP4 -0.4246 -3.7738 0.0498 0.0296 Not Analyzed -4.716 10.8565 BHLHA15_var_2_ 20.20 PKNOX2 KH2012:KH.C4.366 ERF2 -0.4525 -4.0588 -0.4161 -4.1889 Not Analyzed 2.82 9.808 HSF2 17.33 HSF4 KH2012:KH.C7.157 Emc -0.4789 -4.1402 1.5495 19.9980 Not Analyzed No PWM match No PWM match KH2012:KH.L24.23 Myc -0.5105 -4.9445 -0.2157 -3.1476 Not Analyzed -1.1225 No PWM Hits KH2012:KH.C1.1116 NoTrlc -2.4188 -46.8305 -0.5121 -10.5523 Not Analyzed No PWM match No PWM match

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster Plagl1 25.33 Plagl1 GLIS2 20.13 ZIC3 ZNF136 18.78 ZNF136 Esrrg 17.98 ESRRB CUX2 15.47 ONECUT2

A7.3 & A7.7 Primary Notochord Primary Notochord KH2012 TF common name Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.L128.12 Mnx 1.6655 90.0166 Yes 6.095 23.4405 KH2012:KH.S1404.1 2.2991 106.6342 0.8775 20.0875 Yes 0.213 4.3835 KH2012:KH.S1404.1 Brachyury 3.2377 168.2522 1.0937 49.0207 Not Analyzed 8.906 8.906 KH2012:KH.S215.4 Lhx3 1.6162 77.2164 Yes 13.692 23.4405 KH2012:KH.C8.247 ELK 2.1172 99.8324 1.1625 36.9368 No 11.275 26.273 KH2012:KH.C7.269 Orphan bHLH1 1.5312 56.6187 2.3047 68.9936 Not Analyzed No PWM match No PWM match KH2012:KH.C8.247 ELK 1.4388 50.8517 Yes 18.754 30.1065 KH2012:KH.L128.12 Mnx 1.5494 96.7758 -0.1305 -1.0476 Yes -1.25 9.8435 KH2012:KH.C11.313 FoxA-a 1.2823 53.8654 0.3180 0.7099 Not Analyzed 8.88 No PWM Hits KH2012:KH.S1404.1 Brachyury 1.3882 80.0408 Yes 7.002 7.002 KH2012:KH.C11.313 FoxA-a 1.4532 82.5076 0.4067 8.8348 Yes 2.3305 No PWM Hits KH2012:KH.C8.247 ELK 0.6782 25.2655 -0.6333 -23.1942 Not Analyzed 9.611 23.2575 KH2012:KH.C11.313 FoxA-a 0.6946 7.2003 Yes -0.669999999999999 No PWM Hits KH2012:KH.S215.4 Lhx3 0.8037 55.1537 -0.8802 -20.9689 No -2.479 9.8435 KH2012:KH.L4.17 Zinc Finger (C2H2)-18 0.6749 30.9295 1.5500 75.8033 Not Analyzed 5.687 5.687 KH2012:KH.S816.1 ZicL 0.5175 10.1667 No 16.8505 18.475 KH2012:KH.C4.182 Zinc Finger (C3H) 0.5962 23.1657 0.2263 6.6346 No No PWM match No PWM match KH2012:KH.C4.182 Zinc Finger (C3H) 0.5808 9.5566 0.2285 0.1013 Not Analyzed No PWM match No PWM match KH2012:KH.C3.312 E(spl)/hairy-b 0.4487 8.6937 No 3.0535 No PWM Hits KH2012:KH.C3.312 E(spl)/hairy-b 0.5755 15.1531 0.3989 7.0377 No -1.7505 No PWM Hits KH2012:KH.L108.4 CREB/ATF-a 0.5577 14.0799 0.0576 0.1634 Not Analyzed 3.9055 3.9055 KH2012:KH.C4.182 Zinc Finger (C3H) 0.4307 4.4194 No No PWM match No PWM match KH2012:KH.C1.159 E(spl)/hairy-a 0.4487 17.1058 0.3360 8.3396 No -1.7505 No PWM Hits KH2012:KH.L13.24 FoxN2/3 0.4193 12.8049 0.2198 2.7297 Not Analyzed 6.5365 10.528 KH2012:KH.C4.509 Zinc Finger (absent, small, or homeotic discs 1) 0.3968 5.2627 No No PWM match No PWM match KH2012:KH.C3.230 Smad6/7 0.4293 8.7030 0.5589 12.4335 No No PWM match No PWM match KH2012:KH.C7.523 SoxC -0.4378 -13.3666 -0.2034 -10.3675 Not Analyzed No PWM match No PWM match KH2012:KH.S1272.2 ALR-like 0.3749 3.5506 No No PWM match No PWM match KH2012:KH.C7.157 Emc -0.4029 -5.7786 0.5086 9.8394 No No PWM match No PWM match KH2012:KH.C14.278 Zinc Finger (C2H2)-34 -0.4417 -15.5478 -1.2288 -64.8238 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.L39.1 FoxH-b -0.5630 -14.7047 No 5.9045 17.5065 KH2012:KH.C11.485 Irx-B -0.4106 -30.5991 -0.2185 -3.8033 No No PWM Hits No PWM Hits KH2012:KH.C9.580 RAR -0.4515 -20.0356 -0.0601 -5.7882 Not Analyzed 0.2065 4.3815 KH2012:KH.C7.157 Emc -0.5794 -10.4600 No No PWM match No PWM match KH2012:KH.C3.773 Ci-mT -0.4326 -15.2016 -0.4686 -6.4888 No No PWM match No PWM match KH2012:KH.C2.573 Smad1/5 -0.4692 -22.3665 -0.4736 -28.7995 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.C3.773 Ci-mT -0.6323 -19.2629 No No PWM match No PWM match KH2012:KH.L39.1 FoxH-b -0.4930 -25.0471 0.1479 2.1640 No 7.209 7.209 KH2012:KH.C14.307 MyoD -0.5895 -9.7009 0.0459 1.3080 Not Analyzed -6.8785 No PWM Hits KH2012:KH.C11.485 Irx-B -0.6395 -20.3814 No No PWM Hits No PWM Hits KH2012:KH.C6.129 Neurogenin -0.6877 -19.3213 0.0995 4.2912 No -1.05 No PWM Hits KH2012:KH.S654.3 Tbx6b/c/d -0.6099 -11.4537 0.0272 0.2347 Not Analyzed No PWM match No PWM match KH2012:KH.C1.99 SoxB1 -0.7333 -23.0812 No No PWM match No PWM match KH2012:KH.C4.341 FoxB -0.7469 -56.2983 0.0105 0.4616 Yes -1.189 10.1465 KH2012:KH.C11.485 Irx-B -0.6954 -36.3602 -0.0440 -4.8958 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.C4.341 FoxB -0.7924 -29.0822 No 7.577 20.452 KH2012:KH.C1.99 SoxB1 -0.9380 -59.9264 -0.0396 -0.7359 Yes No PWM match No PWM match KH2012:KH.C14.520 Orphan Fox-1 -0.7254 -51.7052 -0.1407 -6.3048 Not Analyzed 1.978 10.528 KH2012:KH.C14.408 Cdx -0.8210 -26.9938 0.0301 0.3522 Not Analyzed 1.4025 3.2205

KH2012:KH.C1.274 MyTF -0.8282 -24.6362 -0.0008 -3.0392 Not Analyzed -4.017 10.5635 KH2012:KH.S816.1 ZicL -0.8853 -47.0900 -0.6984 -38.5394 Not Analyzed -2.693 10.5635 JASPAR 2020 Max Z-score Max Z-score JASPAR 2020 Max Z-score Max Z-score KH2012:KH.C10.113 ets/pointed2 -0.9243 -47.4504 -0.3011 -13.5295 Not Analyzed 12.2195 23.2575 PWM cluster in cluster in cluster PWM cluster in cluster in cluster KH2012:KH.C4.84 Otx -0.9845 -34.4304 -0.2249 -9.3430 Not Analyzed -5.71 7.2085 KH2012:KH.C3.751 Snail -1.0498 -9.6074 -0.1103 -6.0456 Not Analyzed -0.549 9.073 RARA_var_2_ 36.24 RARA::RXRG ELK3 26.27 ETV5 KH2012:KH.C6.129 Neurogenin -1.3685 -23.5590 -0.0746 -4.8043 Not Analyzed 5.3755 No PWM Hits ELK3 30.11 ETV5 PBX3 19.05 PBX3 KH2012:KH.C1.99 SoxB1 -1.4508 -79.9268 -0.2899 -21.0405 Not Analyzed No PWM match No PWM match NFKB2 27.78 REL RARA_var_2_ 18.64 RARA::RXRA KH2012:KH.C1.777 Zinc Finger (C2H2)-33 -1.9472 -64.9976 -0.1098 -7.8661 Not Analyzed -1.385 9.073 Arid5a 25.60 Arid5a GLIS2 17.90 GLI2 GRHL2 23.72 TFCP2 RREB1 16.05 RREB1 PDX1 23.44 NFYB Foxf1 20.45 FOXD2 JASPAR 2020 Max Z-score Max Z-score SP3 20.31 KLF9 PWM cluster in cluster in cluster Esrrg 19.02 ESRRA GLIS2 18.48 ZIC1 ELK3 23.26 ETV2 ZBTB32 17.98 ZBTB32 Stat5a::Stat5b 17.53 BCL6 PITX3 17.51 Dmbx1 VEZF1 16.30 VEZF1 ZBTB6 16.06 ZBTB6 PRDM1 15.97 PRDM1

A9.14 & A9.16 KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C7.157 Emc 0.7689 6.2482 2.2049 30.7597 No No PWM match No PWM match KH2012:KH.L96.11 Groucho2 0.4466 6.9731 -0.1124 -2.2858 No No PWM match No PWM match KH2012:KH.S215.9 Pbx 0.4298 6.2482 0.0103 0.2996 No 9.306 9.306 KH2012:KH.C4.366 ERF2 -0.5128 -5.0576 0.5213 8.5089 No -11.895 11.699 KH2012:KH.C3.312 E(spl)/hairy-b -0.6515 -3.4098 0.6880 8.4803 No -5.544 No PWM Hits KH2012:KH.C1.777 Zinc Finger (C2H2)-33 -0.7830 -7.8216 2.0155 46.5549 No -2.021 12.685 KH2012:KH.C14.408 Cdx -0.9080 -10.0016 0.0340 0.2740 No 1.9715 6.7895 KH2012:KH.C1.274 MyTF -1.3597 -11.8816 0.3472 5.6953 No No PWM Hits 1.712 KH2012:KH.C11.313 FoxA-a -1.3894 -12.0120 -0.0539 -3.2716 No 4.497 No PWM Hits KH2012:KH.C8.247 ELK -1.7787 -20.2806 -0.2236 -10.3022 No -12.7325 11.699 KH2012:KH.L128.12 Mnx -2.1776 -22.1957 0.3413 2.6494 No 1.8955 8.5515

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster FOS::JUNB 47.14 Nfe2l2 Hmx1 19.23 Hmx2 NFIL3 17.79 NFIL3 A8.7 & A8.8 Nr2f6 16.66 LEF1 KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C3.230 Smad6/7 -0.5353 -20.5619 -0.0181 -0.0670 No No PWM match No PWM match KH2012:KH.C6.129 Neurogenin -0.9601 -19.2393 0.2517 14.0525 No -1.995 No PWM Hits KH2012:KH.C7.157 Emc -0.9733 -25.6153 -0.1789 -1.4411 No No PWM match No PWM match KH2012:KH.C3.751 Snail -1.4195 -46.1370 0.2226 9.8066 No 0.5785 8.2395

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster Hmx1 27.64 Hmx2 FOSL2::JUNB_var_2_ 24.02 ATF2 ARNT2 17.59 ATF6 NFIL3 15.80 DBP

A9.13 & A9.15 KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.L128.12 Mnx 2.1776 22.1957 2.5188 37.2324 Yes -1.1495 7.4455 KH2012:KH.C8.247 ELK 1.7787 20.2806 1.5551 14.4166 No 12.75 18.465 KH2012:KH.C11.313 FoxA-a 1.3894 12.0120 1.3355 7.8038 No -3.6455 No PWM Hits KH2012:KH.C1.274 MyTF 1.3597 11.8816 1.7069 26.4929 No -2.915 4.964 KH2012:KH.C14.408 Cdx 0.9080 10.0016 0.9420 14.8548 No -0.8575 5.014 KH2012:KH.C1.777 Zinc Finger (C2H2)-33 0.7830 7.8216 2.7986 47.4718 No 1.5925 10.853 KH2012:KH.C3.312 E(spl)/hairy-b 0.6515 3.4098 1.3395 13.7315 No 4.144 No PWM Hits KH2012:KH.C4.366 ERF2 0.5128 5.0576 1.0341 17.4903 No 11.254 18.465 KH2012:KH.S215.9 Pbx -0.4298 -6.2482 -0.4196 -8.2551 No -4.9205 -2.311 KH2012:KH.L96.11 Groucho2 -0.4466 -6.9731 -0.5590 -12.4908 No No PWM match No PWM match KH2012:KH.C7.157 Emc -0.7689 -6.2482 1.4360 15.6079 No No PWM match No PWM match

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster SP3 23.79 EGR1 ZNF682 20.52 ZNF682 ELK3 18.46 ETV6 Nr2f6 16.75 THRB TFAP2B 15.43 TFAP2A FOSL2::JUNB_var_2_ 15.22 CREM SOX8 15.04 SOX12

A9.29 KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C8.247 ELK 1.7003 16.1584 0.8653 10.4994 No 6.947 22.4835 KH2012:KH.C14.408 Cdx 1.4608 13.2185 1.4608 32.8352 No -1.8375 -0.66 KH2012:KH.C1.777 Zinc Finger (C2H2)-33 1.1084 7.2726 1.4404 17.1069 No 6.48 17.72 KH2012:KH.C1.274 MyTF 0.9215 9.3375 1.0747 29.6455 No No PWM Hits 17.615 KH2012:KH.L128.12 Mnx 0.7398 4.4002 0.7015 6.8642 No 6.1065 16.378 KH2012:KH.C11.313 FoxA-a 0.7116 5.9973 0.4112 0.6187 No -4.2115 No PWM Hits KH2012:KH.S816.1 ZicL 0.5255 3.8962 0.2625 1.4167 Yes 17.615 17.615 A7.4 & A7.8 KH2012:KH.C3.312 E(spl)/hairy-b 0.5071 5.4824 0.9983 20.8870 No 1.2415 No PWM Hits KH2012:KH.S1404.1 Brachyury 0.4808 3.3931 0.4808 8.7273 No -0.112 5.468 KH2012 TF common name Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012:KH.C4.182 Zinc Finger (C3H) 0.4090 3.8159 0.3772 2.9396 No No PWM match No PWM match gene model Sibling Cluster Sibling Cluster z-score z-score KH2012:KH.C9.68 Pax6 -0.8588 -8.7177 0.0338 1.9885 No 8.08 8.08 KH2012:KH.C4.341 FoxB 0.7924 29.0822 Yes -4.719 3.1885 KH2012:KH.C7.157 Emc -1.2267 -8.8583 -0.4219 -5.0309 No No PWM match No PWM match KH2012:KH.C1.99 SoxB1 0.7333 23.0812 No No PWM match No PWM match KH2012:KH.C11.485 Irx-B 0.6395 20.3814 Yes No PWM Hits No PWM Hits KH2012:KH.C3.773 Ci-mT 0.6323 19.2629 No No PWM match No PWM match KH2012:KH.C7.157 Emc 0.5794 10.4600 No No PWM match No PWM match JASPAR 2020 Max Z-score Max Z-score KH2012:KH.L39.1 FoxH-b 0.5630 14.7047 No -3.392 0.3995 PWM cluster in cluster in cluster KH2012:KH.S1272.2 ALR-like -0.3749 -3.5506 No No PWM match No PWM match ESR1 27.38 ESR2 KH2012:KH.C4.509 Zinc Finger (absent, small, or homeotic discs 1) -0.3968 -5.2627 No No PWM match No PWM match Esrrg 23.93 ESRRA KH2012:KH.C4.182 Zinc Finger (C3H) -0.4307 -4.4194 No No PWM match No PWM match ELK3 22.48 ETV2 KH2012:KH.C3.312 E(spl)/hairy-b -0.4487 -8.6937 No -2.0615 No PWM Hits MEF2D 19.57 MEF2A KH2012:KH.S816.1 ZicL -0.5175 -10.1667 No -5.858 3.7785 Hand1::Tcf3 19.20 SMAD2::SMAD3::SMAD4 KH2012:KH.C11.313 FoxA-a -0.6946 -7.2003 No 0.5975 No PWM Hits BHLHA15_var_2_ 17.72 PKNOX2 KH2012:KH.S1404.1 Brachyury -1.3882 -80.0408 No -3.1585 -3.1585 GLIS2 17.62 ZIC4 KH2012:KH.C8.247 ELK -1.4388 -50.8517 No -7.679 3.0945 MAFG 17.40 MAFG KH2012:KH.S215.4 Lhx3 -1.6162 -77.2164 No -7.079 4.492 FOS::JUNB 17.06 FOSL1::JUNB KH2012:KH.L128.12 Mnx -1.6655 -90.0166 No -4.0275 4.492 PDX1 16.38 POU6F1 NKX2-3 15.85 MSANTD3 SP3 15.18 EGR1

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster ZBED1 15.96 ZBED1 NR3C1 15.68 Ar

A9.30 KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C7.157 Emc 1.2267 8.8583 0.8048 5.4243 No No PWM match No PWM match KH2012:KH.C9.68 Pax6 0.8588 8.7177 0.8926 19.8954 Yes -4.3105 6.9875 KH2012:KH.C4.182 Zinc Finger (C3H) -0.4090 -3.8159 -0.0318 -2.0008 No No PWM match No PWM match KH2012:KH.C3.312 E(spl)/hairy-b -0.5071 -5.4824 0.4913 1.6543 No -0.8255 No PWM Hits KH2012:KH.S816.1 ZicL -0.5255 -3.8962 -0.2629 -2.2808 No -5.4215 2.076 KH2012:KH.C11.313 FoxA-a -0.7116 -5.9973 -0.3004 -6.6630 No 3.064 No PWM Hits KH2012:KH.L128.12 Mnx -0.7398 -4.4002 -0.0383 -1.0801 No -3.8375 4.33 KH2012:KH.C1.274 MyTF -0.9215 -9.3375 0.1532 2.6280 No -2.847 2.076 KH2012:KH.C1.777 Zinc Finger (C2H2)-33 -1.1084 -7.2726 0.3320 0.1220 No -3.19 7.569 KH2012:KH.C8.247 ELK -1.7003 -16.1584 -0.8350 -11.4898 No -3.825 24.249

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster ELK3 24.25 SPI1 Rarg_var_2_ 19.01 Nr1h3::Rxra SRF 17.38 SRF NR1I2 17.36 NR1I2

A8.15 & A8.16 KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C3.751 Snail 1.4195 46.1370 1.6420 100.2606 Yes -1.0215 18.0355 KH2012:KH.C7.157 Emc 0.9733 25.6153 0.7944 25.0689 No No PWM match No PWM match KH2012:KH.C6.129 Neurogenin 0.9601 19.2393 1.2117 64.2736 Yes 3.956 No PWM Hits KH2012:KH.C3.230 Smad6/7 0.5353 20.5619 0.5173 27.7359 No No PWM match No PWM match

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster TFAP2B 25.77 TFAP2C Zic1::Zic2 24.17 Zic1::Zic2 RUNX1 20.80 RUNX2 RFX2 20.67 RFX1 HSF2 20.64 ZBTB12 GFI1 18.44 Gfi1b SMAD3 18.14 Smad4 BHLHA15_var_2_ 18.04 Twist2 Hand1::Tcf3 17.88 SMAD2::SMAD3::SMAD4 NRF1 17.64 NRF1 TP73 17.18 TP63 PDX1 17.18 NFYB Stat5a::Stat5b 17.04 Stat5b ELK3 15.85 ELF3 HINFP 15.66 HINFP ZBTB7B 15.22 ZBTB7B RXRG_var_2_ 15.05 PAX5 A9.31 KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.S654.3 Tbx6b/c/d 2.3930 19.9861 2.3930 50.8180 Not Analyzed No PWM match No PWM match KH2012:KH.C14.307 MyoD 2.2961 19.9861 2.2349 46.7356 Not Analyzed -35.8875 No PWM Hits KH2012:KH.C14.408 Cdx 1.7001 15.2549 1.7001 40.6414 Not Analyzed 19.4445 19.4445 KH2012:KH.C8.247 ELK 1.0639 9.7754 1.2649 20.4751 Not Analyzed 4.2035 28.7595 KH2012:KH.C2.290 GABPα 0.9182 11.2979 0.1723 0.0489 Not Analyzed 20.487 28.7595 KH2012:KH.C1.274 MyTF 0.8646 9.2402 0.8570 24.4488 Not Analyzed No PWM Hits 20.514 KH2012:KH.L13.24 FoxN2/3 0.7777 6.2351 -0.0148 -1.1855 Not Analyzed 2.1675 36.211 KH2012:KH.S423.6 SMYD1 0.7163 6.8082 0.6834 14.8149 Not Analyzed No PWM match No PWM match KH2012:KH.C4.366 ERF2 0.7136 5.3420 1.0117 16.4745 Not Analyzed 3.816 28.7595 KH2012:KH.C13.138 CREB/ATF-d 0.6308 5.6868 -0.1389 -1.4718 Not Analyzed No PWM match No PWM match KH2012:KH.C1.27 LAG1-like1 0.5791 6.9034 -0.1134 -0.8016 Not Analyzed No PWM match No PWM match KH2012:KH.L96.52 transcription factor4 0.5683 6.0008 -0.1296 -1.2142 Not Analyzed 4.925 28.1015 KH2012:KH.C2.822 /2/3/6 0.5528 3.8164 -0.0397 -1.0928 Not Analyzed No PWM match No PWM match KH2012:KH.L99.12 SREBP 0.5422 4.4352 0.4078 2.3589 Not Analyzed No PWM match No PWM match KH2012:KH.C3.137 ATF4/5 0.4529 5.8113 0.2296 1.9003 Not Analyzed No PWM match No PWM match KH2012:KH.S215.9 Pbx 0.4490 3.5928 -0.0910 -0.0926 Not Analyzed -6.412 21.702 KH2012:KH.L155.15 SWI/SNF 0.4461 3.0665 0.0001 0.6238 Not Analyzed No PWM match No PWM match KH2012:KH.C4.83 HIF 0.4151 3.8190 0.3687 1.8965 Not Analyzed No PWM match No PWM match KH2012:KH.C1.264 Y-box protein1/2/3 -0.5797 -4.5783 0.3849 5.9844 Not Analyzed No PWM match No PWM match KH2012:KH.C6.129 Neurogenin -0.8473 -5.9149 1.3959 21.3158 Not Analyzed 6.9525 No PWM Hits KH2012:KH.C7.269 Orphan bHLH1 -0.9321 -4.0901 0.0338 1.0833 Not Analyzed No PWM match No PWM match KH2012:KH.C3.751 Snail -1.4414 -16.3211 0.7190 10.9530 Not Analyzed 7.0085 28.4005 KH2012:KH.L24.10 COE -1.9797 -11.2277 0.0793 3.5708 Not Analyzed -4.0065 8.993 KH2012:KH.C7.157 Emc -2.7990 -12.3290 -0.6245 -17.4969 Not Analyzed No PWM match No PWM match

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster Esrrg 38.89 NR2F1 ZNF274 37.95 ZNF274 Foxf1 36.21 FOXL1 Nr2f6 33.49 TCF7L1 TBP 30.33 TBP ELK3 28.76 ELF1 BHLHA15_var_2_ 28.40 MXI1 ARNT2 28.10 CLOCK NFIL3 27.48 NFIL3 SP3 26.27 SP1 OVOL2 26.11 MYBL1 NFKB2 23.24 NFKB1 MEIS1_var_2_ 21.70 PBX2 Arid5a 21.62 Arid5a GLIS2 20.51 GLIS2 GATA2 20.44 GATA4 HOXD10 19.44 CDX2 MEF2D 19.05 MEF2C TBX21 19.02 TBX2 IRF8 18.83 IRF2 ZSCAN4 17.62 ZSCAN4 SMAD3 17.55 ZSCAN29 POU4F1 17.33 BARX2 SRF 16.81 SRF TEAD4 16.55 TEAD2 ZBTB32 16.37 ZBTB32 Plagl1 15.95 PLAGL2 PHOX2A 15.77 DUX4

A9.32 KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C7.157 Emc 2.7990 12.3290 2.1745 13.0587 No No PWM match No PWM match KH2012:KH.L24.10 COE 1.9797 11.2277 2.0590 27.4787 Yes 2.397 10.5995 KH2012:KH.C3.751 Snail 1.4414 16.3211 2.1604 25.0321 No -2.7395 15.3035 KH2012:KH.C7.269 Orphan bHLH1 0.9321 4.0901 0.9659 9.6237 No No PWM match No PWM match KH2012:KH.C6.129 Neurogenin 0.8473 5.9149 2.2432 17.1719 No -2.445 No PWM Hits KH2012:KH.C1.264 Y-box protein1/2/3 0.5797 4.5783 0.9646 9.9919 No No PWM match No PWM match KH2012:KH.C4.83 HIF -0.4151 -3.8190 -0.0464 -3.8550 No No PWM match No PWM match KH2012:KH.L155.15 SWI/SNF -0.4461 -3.0665 -0.4460 -5.4321 No No PWM match No PWM match KH2012:KH.S215.9 Pbx -0.4490 -3.5928 -0.5400 -4.8068 No 2.2545 4.539 KH2012:KH.C3.137 ATF4/5 -0.4529 -5.8113 -0.2233 -5.3507 No No PWM match No PWM match KH2012:KH.L99.12 SREBP -0.5422 -4.4352 -0.1344 -5.1675 No No PWM match No PWM match KH2012:KH.C2.822 E2F1/2/3/6 -0.5528 -3.8164 -0.5925 -6.5405 No No PWM match No PWM match KH2012:KH.L96.52 transcription factor4 -0.5683 -6.0008 -0.6979 -10.4778 No -1.64 12.8595 KH2012:KH.C1.27 LAG1-like1 -0.5791 -6.9034 -0.6925 -11.7964 No No PWM match No PWM match KH2012:KH.C13.138 CREB/ATF-d -0.6308 -5.6868 -0.7698 -10.0326 No No PWM match No PWM match KH2012:KH.C4.366 ERF2 -0.7136 -5.3420 0.2980 1.6819 No -1.4445 4.622 KH2012:KH.S423.6 SMYD1 -0.7163 -6.8082 -0.0329 -0.9833 No No PWM match No PWM match KH2012:KH.L13.24 FoxN2/3 -0.7777 -6.2351 -0.7925 -9.1548 No -0.8145 2.9055 KH2012:KH.C1.274 MyTF -0.8646 -9.2402 -0.0076 -0.4720 No No PWM Hits 9.72 KH2012:KH.C2.290 GABPα -0.9182 -11.2979 -0.7459 -15.0839 No -6.73 4.622 KH2012:KH.C8.247 ELK -1.0639 -9.7754 0.2010 1.1294 No -1.674 4.622 KH2012:KH.C14.307 MyoD -2.2961 -19.9861 -0.0611 -1.2037 No 17.0255 No PWM Hits

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster MAFG 18.88 MAFF FOS::JUNB 17.74 MAFA BHLHA15_var_2_ 15.30 Tcf12

B7.4 B7.4 Muscle B7.4 Muscle KH2012 TF common name Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C14.307 MyoD 1.0114 38.3730 Yes 5.4255 No PWM Hits KH2012:KH.S423.6 SMYD1 2.5557 69.2856 2.1486 27.0958 Yes No PWM match No PWM match KH2012:KH.S423.6 SMYD1 4.2339 72.5208 2.1729 53.5000 Not Analyzed No PWM match No PWM match KH2012:KH.S423.6 SMYD1 0.6637 22.6222 Yes No PWM match No PWM match KH2012:KH.C14.307 MyoD 1.4595 63.7051 0.5156 7.7329 Yes 17.715 No PWM Hits KH2012:KH.S654.3 Tbx6b/c/d 2.3405 59.5102 0.9660 26.1380 Not Analyzed No PWM match No PWM match KH2012:KH.C3.773 Ci-mT 0.6566 10.7795 No No PWM match No PWM match KH2012:KH.S654.3 Tbx6b/c/d 1.3246 41.3078 0.9754 15.2567 Yes No PWM match No PWM match KH2012:KH.C14.307 MyoD 1.9656 61.2800 0.4237 6.2956 Not Analyzed 31.2315 No PWM Hits KH2012:KH.S654.3 Tbx6b/c/d 0.5474 10.7698 No No PWM match No PWM match KH2012:KH.C3.773 Ci-mT 0.7602 23.0387 -0.1111 -0.6917 No No PWM match No PWM match KH2012:KH.C14.377 Otp 1.9450 54.6311 1.4978 29.8833 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.L4.17 Zinc Finger (C2H2)-18 0.4438 1.7420 No -8.994 -8.994 KH2012:KH.C4.341 FoxB 0.5871 36.3532 0.2656 4.2335 No -3.599 1.9255 KH2012:KH.L128.12 Mnx 1.6029 44.7975 1.7134 36.4249 Not Analyzed 5.467 12.1825 KH2012:KH.C4.341 FoxB 0.3863 12.0362 No 0.00350000000000028 7.4625 KH2012:KH.C14.377 Otp 0.5704 49.7838 0.5215 13.9877 Yes No PWM Hits No PWM Hits KH2012:KH.C3.751 Snail 1.5588 47.3654 1.2625 39.9622 Not Analyzed -2.4785 43.593 KH2012:KH.C6.22 Smad2/3a 0.3649 3.2196 No No PWM match No PWM match KH2012:KH.S816.1 ZicL 0.5423 15.2565 0.0650 0.4472 No 14.3105 14.3105 KH2012:KH.C1.264 Y-box protein1/2/3 0.8454 25.5557 1.1022 32.9988 Not Analyzed No PWM match No PWM match KH2012:KH.C4.84 Otx -0.4023 -3.3627 No -3.4615 4.088 KH2012:KH.C3.751 Snail 0.4889 14.6274 0.6950 13.7913 No -0.843 31.494 KH2012:KH.C3.17 ROR 0.6593 14.6226 1.2754 34.4470 Not Analyzed 1.592 14.2665 KH2012:KH.L128.12 Mnx -0.4326 -7.5112 No 0.398 8.732 KH2012:KH.C1.159 E(spl)/hairy-a -0.4360 -3.2345 0.1433 4.0304 Yes 4.3655 No PWM Hits KH2012:KH.C4.83 HIF 0.6118 19.0139 0.3437 3.7205 Not Analyzed No PWM match No PWM match KH2012:KH.S215.4 Lhx3 -0.4536 -8.5864 No -1.0935 8.732 KH2012:KH.C5.416 TWIST-like-1a/b -0.4684 -5.9869 0.0695 1.8496 No No PWM match No PWM match KH2012:KH.C11.485 Irx-B 0.5340 9.1902 0.6363 1.9434 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.S1404.1 Brachyury -0.4584 -6.0576 No No PWM Hits No PWM Hits KH2012:KH.C4.84 Otx -0.5337 -4.5675 0.1831 0.9549 No 5.0875 5.0875 KH2012:KH.C9.717 FoxH-a 0.5293 15.7581 0.5128 11.3849 Not Analyzed -5.979 0.4025 KH2012:KH.C8.247 ELK -0.4978 -6.4705 No -1.708 14.204 KH2012:KH.L128.12 Mnx -0.6309 -11.2695 0.0398 1.8243 No 0.6555 14.0475 KH2012:KH.S899.4 BTF3 0.5269 15.5987 0.5246 18.6919 Not Analyzed No PWM match No PWM match KH2012:KH.C11.485 Irx-B -0.6819 -12.7045 No No PWM Hits No PWM Hits KH2012:KH.C11.313 FoxA-a -0.8414 -11.2378 -0.2246 -2.3258 No -1.0375 No PWM Hits KH2012:KH.C10.113 ets/pointed2 0.5017 12.1479 -0.0118 -0.9834 Not Analyzed -20.2045 -0.293 KH2012:KH.S1404.1 Brachyury -1.2130 -13.6116 0.0129 0.5959 No 0.958 0.958 KH2012:KH.C9.580 RAR 0.4172 11.0439 0.3663 2.4978 Not Analyzed 1.2875 4.7925

KH2012:KH.L108.4 CREB/ATF-a -0.4206 -4.2396 -0.1429 -3.4178 Not Analyzed 4.1955 14.013 KH2012:KH.C7.207 FoxP -0.4719 -6.2525 -0.0563 -3.6403 Not Analyzed -5.6795 -0.7195 JASPAR 2020 Max Z-score Max Z-score KH2012:KH.C9.38 FUBP -0.5001 -3.9912 -0.0226 -2.1237 Not Analyzed No PWM match No PWM match PWM cluster in cluster in cluster JASPAR 2020 Max Z-score Max Z-score KH2012:KH.L171.10 Hex -0.6248 -14.0727 -0.0072 -1.6620 Not Analyzed No PWM match No PWM match PWM cluster in cluster in cluster KH2012:KH.C1.959 Hox4 -0.6931 -15.5710 0.0203 0.3566 Not Analyzed No PWM Hits No PWM Hits Esrrg 26.56 NR2F1 KH2012:KH.C1.159 E(spl)/hairy-a -0.7448 -9.8788 0.1089 2.5909 Not Analyzed -4.0045 No PWM Hits FOS::JUNB 24.33 JUND ARNT2 34.15 HES5 KH2012:KH.C4.182 Zinc Finger (C3H) -0.9693 -16.0501 -0.0255 -2.2649 Not Analyzed No PWM match No PWM match TP73 20.95 TP73 BHLHA15_var_2_ 31.49 ASCL1 KH2012:KH.C3.312 E(spl)/hairy-b -0.9764 -14.4634 0.3864 3.9129 Not Analyzed -4.0045 No PWM Hits TBX21 16.99 TBX18 SP3 30.13 Klf1 KH2012:KH.C7.269 Orphan bHLH1 -1.4744 -5.9806 0.1037 0.1723 Not Analyzed No PWM match No PWM match ARNT2 16.41 MITF POU4F1 29.50 HNF1A KH2012:KH.C11.314 Fos -1.5948 -20.5905 0.0198 0.5684 Not Analyzed -5.8115 15.304 PHOX2A 25.63 DUXA KH2012:KH.C8.247 ELK -1.6548 -36.4868 -0.1389 -4.6729 Not Analyzed -12.9125 -0.293 IRF8 24.83 IRF2 KH2012:KH.C4.539 Fli/ERG1 -1.6879 -28.8136 0.0356 0.7803 Not Analyzed -20.0155 -0.293 E2F7 24.69 KH2012:KH.C11.313 FoxA-a -2.0324 -44.5504 0.0445 5.3453 Not Analyzed -7.622 No PWM Hits SRF 24.24 SRF KH2012:KH.C5.416 TWIST-like-1a/b -2.3534 -29.7826 -0.0422 -2.0990 Not Analyzed No PWM match No PWM match Nr2f6 21.88 Rxra KH2012:KH.S1404.1 Brachyury -2.5992 -27.5247 -0.0373 -4.8754 Not Analyzed 5.736 5.736 Esrrg 18.86 ESRRA MEIS1_var_2_ 18.59 PBX2 TBX21 17.82 TBX6 MEIS3 15.83 MEIS3 JASPAR 2020 Max Z-score Max Z-score TP73 15.69 TP73 PWM cluster in cluster in cluster NKX2-3 15.35 Nkx3-2 BHLHA15_var_2_ 43.59 Ascl2 RREB1 20.14 RREB1 DMRTC2 18.98 DMRTA2 TBX21 18.91 MGA NR1I2 17.11 RXRA::VDR SOX8 15.93 SOX21 FOS::JUNB 15.30 MAFK

B8.5 B8.5 Mesenchyme KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C5.416 TWIST-like-1a/b 0.4650 12.2478 0.8098 28.3701 Yes No PWM match No PWM match KH2012:KH.C5.202 TWIST-like-2 3.1346 30.4991 3.1346 33.3568 Not Analyzed No PWM match No PWM match KH2012:KH.S980.1 Zinc finger (PHD)-2 -0.5060 -9.2184 0.2276 3.5230 No No PWM match No PWM match KH2012:KH.C5.416 TWIST-like-1a/b 3.1286 29.3880 2.3089 21.6133 Not Analyzed No PWM match No PWM match KH2012:KH.C8.247 ELK -0.7425 -3.0149 0.7597 13.9336 Yes -3.5855 7.0875 KH2012:KH.C4.539 Fli/ERG1 2.3891 27.2417 2.3817 29.2285 Not Analyzed 10.7655 24.525 KH2012:KH.C11.314 Fos 2.3246 24.2036 2.2749 24.3551 Not Analyzed 1.563 9.531 KH2012:KH.C4.84 Otx 1.1108 12.0797 -0.1274 -1.2896 Not Analyzed 6.3415 9.9375 KH2012:KH.C11.657 Hlx 1.0441 8.5204 1.0441 9.4342 Not Analyzed No PWM Hits No PWM Hits JASPAR 2020 Max Z-score Max Z-score KH2012:KH.L171.10 Hex 0.9984 11.1230 0.9984 12.3084 Not Analyzed No PWM match No PWM match PWM cluster in cluster in cluster KH2012:KH.C1.959 Hox4 0.8713 8.1026 1.0590 13.0640 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.C1.159 E(spl)/hairy-a 0.7856 7.3834 0.7375 3.5497 Not Analyzed -1.533 No PWM Hits NR3C1 25.53 Ar KH2012:KH.C4.182 Zinc Finger (C3H) 0.7706 4.5707 1.0482 4.1204 Not Analyzed No PWM match No PWM match PLAG1 16.32 PLAG1 KH2012:KH.C7.702 Zinc Finger (BTB/POZ) 0.7582 4.7434 -0.4236 -5.9386 Not Analyzed 8.1725 No PWM Hits ARNT2 15.80 ARNT::HIF1A KH2012:KH.C11.485 Irx-B 0.7233 4.9226 0.1282 2.3192 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.L24.23 Myc 0.6451 4.6522 0.2670 0.2404 Not Analyzed 1.865 No PWM Hits KH2012:KH.C14.278 Zinc Finger (C2H2)-34 0.5663 5.0201 -0.5526 -7.8181 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.C10.113 ets/pointed2 0.5564 3.4252 -0.0477 -2.8432 Not Analyzed 9.851 24.525 KH2012:KH.S215.9 Pbx 0.4398 3.0346 -0.0707 -0.9695 Not Analyzed -4.93 4.1825 KH2012:KH.C7.50 TSC22 -0.4519 -3.3234 -0.0705 -4.4443 Not Analyzed No PWM match No PWM match KH2012:KH.C1.1025 NF-X-like -0.4790 -3.3135 -0.4181 -6.3402 Not Analyzed No PWM match No PWM match KH2012:KH.L18.112 Zinc finger (PHD/NFX, DDT) -0.5454 -5.1078 0.3228 0.0466 Not Analyzed No PWM match No PWM match KH2012:KH.C7.157 Emc -0.7456 -8.6442 0.1792 1.2568 Not Analyzed No PWM match No PWM match KH2012:KH.C3.230 Smad6/7 -0.8059 -9.5696 -0.3794 -13.4257 Not Analyzed No PWM match No PWM match KH2012:KH.L4.17 Zinc Finger (C2H2)-18 -1.3854 -14.7263 0.9071 12.7619 Not Analyzed 9.023 9.023 KH2012:KH.C7.269 Orphan bHLH1 -2.3407 -12.7535 0.0955 0.5492 Not Analyzed No PWM match No PWM match KH2012:KH.S1404.1 Brachyury -3.2554 -24.9264 -0.1685 -6.6093 Not Analyzed 0.9345 11.757

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster ELK3 24.52 ETV5 B7.3 NFIA 21.77 NFIC GCM2 18.12 CENPB KH2012 TF common name Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster Esrrg 16.06 ESRRA gene model Sibling Cluster Sibling Cluster z-score z-score KH2012:KH.C11.485 Irx-B 0.6819 12.7045 No No PWM Hits No PWM Hits KH2012:KH.C8.247 ELK 0.4978 6.4705 Yes 1.3575 12.0935 KH2012:KH.S1404.1 Brachyury 0.4584 6.0576 No -5.753 -5.575 KH2012:KH.S215.4 Lhx3 0.4536 8.5864 Yes 0.7965 14.3175 KH2012:KH.L128.12 Mnx 0.4326 7.5112 Yes -0.491 14.3175 KH2012:KH.C4.84 Otx 0.4023 3.3627 Yes 2.6675 9.053 KH2012:KH.C6.22 Smad2/3a -0.3649 -3.2196 No No PWM match No PWM match KH2012:KH.C4.341 FoxB -0.3863 -12.0362 No 0.2515 5.15 KH2012:KH.L4.17 Zinc Finger (C2H2)-18 -0.4438 -1.7420 No No PWM Hits No PWM Hits KH2012:KH.S654.3 Tbx6b/c/d -0.5474 -10.7698 No No PWM match No PWM match KH2012:KH.C3.773 Ci-mT -0.6566 -10.7795 No No PWM match No PWM match KH2012:KH.S423.6 SMYD1 -0.6637 -22.6222 No No PWM match No PWM match KH2012:KH.C14.307 MyoD -1.0114 -38.3730 No -3.8555 No PWM Hits

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster YY1 22.50 ZFP42 Wt1 20.73 ZNF263 Nr2f6 15.43 Pparg::Rxra

B8.6 Secondary Notochord KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C8.247 ELK 0.7425 3.0149 1.5022 19.6229 No 7.678 8.7995 KH2012:KH.S1404.1 Brachyury 3.2554 24.9264 2.0112 17.6374 Not Analyzed -0.7905 -0.7905 KH2012:KH.S980.1 Zinc finger (PHD)-2 0.5060 9.2184 0.7336 22.8094 No No PWM match No PWM match KH2012:KH.C7.269 Orphan bHLH1 2.3407 12.7535 2.3331 19.1992 Not Analyzed No PWM match No PWM match KH2012:KH.C5.416 TWIST-like-1a/b -0.4650 -12.2478 0.3449 4.9897 No No PWM match No PWM match KH2012:KH.L4.17 Zinc Finger (C2H2)-18 1.3854 14.7263 1.9327 26.1059 Not Analyzed -5.302 -5.302 KH2012:KH.C3.230 Smad6/7 0.8059 9.5696 0.2565 2.0676 Not Analyzed No PWM match No PWM match KH2012:KH.C7.157 Emc 0.7456 8.6442 0.5495 2.6210 Not Analyzed No PWM match No PWM match KH2012:KH.L18.112 Zinc finger (PHD/NFX, DDT) 0.5454 5.1078 0.4546 3.1098 Not Analyzed No PWM match No PWM match JASPAR 2020 Max Z-score Max Z-score KH2012:KH.C1.1025 NF-X-like 0.4790 3.3135 0.0579 0.1435 Not Analyzed No PWM match No PWM match PWM cluster in cluster in cluster KH2012:KH.C7.50 TSC22 0.4519 3.3234 0.3568 1.1147 Not Analyzed No PWM match No PWM match KH2012:KH.S215.9 Pbx -0.4398 -3.0346 -0.5318 -5.7347 Not Analyzed 4.66 4.66 E2F7 35.99 E2F8 KH2012:KH.C10.113 ets/pointed2 -0.5564 -3.4252 -0.7857 -12.3141 Not Analyzed -7.57 8.651 SP3 31.97 ZBTB14 KH2012:KH.C14.278 Zinc Finger (C2H2)-34 -0.5663 -5.0201 -1.0967 -16.2653 Not Analyzed No PWM Hits No PWM Hits FOS::JUNB 26.29 MAFK KH2012:KH.L24.23 Myc -0.6451 -4.6522 -0.5708 -7.2547 Not Analyzed -1.6285 No PWM Hits Wt1 22.58 ZNF263 KH2012:KH.C11.485 Irx-B -0.7233 -4.9226 -0.7899 -11.1356 Not Analyzed No PWM Hits No PWM Hits MAFG 20.77 MAFF KH2012:KH.C7.702 Zinc Finger (BTB/POZ) -0.7582 -4.7434 -1.0504 -16.0129 Not Analyzed -5.6875 No PWM Hits RARA_var_2_ 18.66 RARA::RXRA KH2012:KH.C4.182 Zinc Finger (C3H) -0.7706 -4.5707 0.2572 1.3077 Not Analyzed No PWM match No PWM match ZNF143 18.50 ZNF143 KH2012:KH.C1.159 E(spl)/hairy-a -0.7856 -7.3834 -0.0676 -1.4341 Not Analyzed 1.3295 No PWM Hits GRHL2 15.89 GRHL2 KH2012:KH.C1.959 Hox4 -0.8713 -8.1026 0.1561 2.6464 Not Analyzed No PWM Hits No PWM Hits GCM2 15.39 CENPB KH2012:KH.C4.84 Otx -1.1108 -12.0797 -1.0476 -15.7432 Not Analyzed -5.1455 0.0985 KH2012:KH.C11.314 Fos -2.3246 -24.2036 -0.0136 -0.6987 Not Analyzed -1.3845 12.401 KH2012:KH.C4.539 Fli/ERG1 -2.3891 -27.2417 -0.0355 -0.6987 Not Analyzed -8.4515 8.651 KH2012:KH.C5.416 TWIST-like-1a/b -3.1286 -29.3880 -0.3548 -3.1606 Not Analyzed No PWM match No PWM match KH2012:KH.C5.202 TWIST-like-2 -3.1346 -30.4991 -0.0347 -0.6987 Not Analyzed No PWM match No PWM match

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster CUX2 35.41 ONECUT2 POU3F1 18.47 POU2F3 TFAP2B 15.45 TFAP2C

B7.6 B7.6 B7.6 KH2012 TF common name Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C1.727 macho-1 2.3339 44.9245 No 1.676 No PWM Hits KH2012:KH.C1.727 macho-1 3.8125 14.1546 1.3329 6.9233 No -2.615 No PWM Hits KH2012:KH.C1.727 macho-1 3.4617 18.5699 -0.5170 -1.2414 Not Analyzed -0.7225 No PWM Hits KH2012:KH.C1.1016 GCNF 0.9014 11.4726 No No PWM match No PWM match KH2012:KH.C1.777 Zinc Finger (C2H2)-33 1.9082 10.1472 1.6216 8.7439 No 4.8635 5.765 KH2012:KH.C1.1016 GCNF 2.1354 10.9785 1.1260 2.4206 Not Analyzed No PWM match No PWM match KH2012:KH.C8.450 Nkx-A 0.7090 10.5529 No No PWM match No PWM match KH2012:KH.C1.1016 GCNF 1.3337 4.9628 0.3924 1.3573 No No PWM match No PWM match KH2012:KH.C8.450 Nkx-A 1.1482 4.7606 0.2336 0.1865 Not Analyzed No PWM match No PWM match KH2012:KH.C1.777 Zinc Finger (C2H2)-33 0.5126 6.3127 No -1.0775 14.5305 KH2012:KH.C10.92 Baf57 1.1650 16.5951 1.1121 9.0054 No No PWM match No PWM match KH2012:KH.S437.3 Zinc Finger (C2H2)-10 -0.4622 -3.1992 -0.1180 -0.8391 Not Analyzed -4.405 -4.405 KH2012:KH.C11.351 NF45 0.3846 3.9428 No No PWM match No PWM match KH2012:KH.C7.334 Gli 0.8588 5.6709 0.8382 9.2986 No -2.691 7.8225 KH2012:KH.C6.223 E2F4/5 -0.4817 -3.2690 -0.2920 -1.7611 Not Analyzed -6.611 5.101 KH2012:KH.C1.677 Smcx/SMCY/PLU-1/RBP-2 like 1 -0.3871 -3.7430 No No PWM match No PWM match KH2012:KH.S1159.1 Fli/ERG4 0.5398 4.4990 0.5688 7.6018 No No PWM match No PWM match KH2012:KH.L60.12 Dp-1 -0.5570 -4.1963 -0.2882 -1.4451 Not Analyzed No PWM match No PWM match KH2012:KH.S406.15 -0.4144 -2.4656 No -1.075 2.342 KH2012:KH.C4.810 HSF 0.4277 3.0314 0.6269 6.0219 No No PWM match No PWM match KH2012:KH.C1.275 STAT-b -0.5620 -3.4069 -0.3208 -1.3889 Not Analyzed No PWM match No PWM match KH2012:KH.C3.103 RBP1-like -0.4240 -8.3677 No No PWM match No PWM match KH2012:KH.L20.34 Mnt-like -0.4375 -3.1146 -0.3634 -1.4258 No No PWM match No PWM match KH2012:KH.C11.450 CBF -0.5682 -3.9961 0.0778 0.2191 Not Analyzed No PWM match No PWM match KH2012:KH.C3.697 Zinc Finger (C2H2)-5 -0.4955 -4.1111 No -3.3535 3.6845 KH2012:KH.L18.112 Zinc finger (PHD/NFX, DDT) -0.5084 -3.0771 -0.3639 -0.8047 No No PWM match No PWM match KH2012:KH.L128.12 Mnx -0.6022 -3.8015 0.1322 0.0000 Not Analyzed -2.3025 8.5955 KH2012:KH.C9.892 RXR -0.4978 -2.6395 No 3.163 10.7925 KH2012:KH.C3.402 IRF-like7 -0.5208 -3.1146 -0.3690 -1.6881 No No PWM match No PWM match KH2012:KH.L165.2 HIV TAT specific factor 1 (HTATSF1) -0.6164 -5.6263 0.5776 0.6711 Not Analyzed No PWM match No PWM match KH2012:KH.C7.157 Emc -0.5819 -4.5001 No No PWM match No PWM match KH2012:KH.S899.4 BTF3 -0.5364 -3.2760 -0.7524 -4.6803 No No PWM match No PWM match KH2012:KH.C1.661 MAD -0.6263 -4.3790 0.0505 0.0000 Not Analyzed No PWM match No PWM match KH2012:KH.C3.312 E(spl)/hairy-b -0.6040 -6.9172 No -1.0715 No PWM Hits KH2012:KH.C10.49 Bcl3 -0.5406 -4.0795 -0.3274 -1.4258 No No PWM match No PWM match KH2012:KH.L53.12 Zinc Finger (C2H2)-15 -0.6325 -4.4759 -0.5963 -3.2099 Not Analyzed 2.4155 2.4155 KH2012:KH.S816.1 ZicL -0.7631 -11.8046 No -9.1325 9.7885 KH2012:KH.L87.58 Zinc Finger (C2H2)-4 -0.5430 -3.8250 -0.8355 -3.3150 No No PWM Hits No PWM Hits KH2012:KH.C8.920 TR2/4 -0.6336 -3.3469 -0.6659 -2.2759 Not Analyzed -1.0795 5.817 KH2012:KH.C3.751 Snail -0.7634 -8.3360 No 2.0075 14.5305 KH2012:KH.L122.11 metastasis associated -0.5496 -3.3639 -0.1269 -0.3287 No No PWM match No PWM match KH2012:KH.C5.130 Zinc Finger (C2H2)-27 -0.6704 -3.0017 -0.4047 -1.1100 Not Analyzed -2.374 12.0705 KH2012:KH.S654.3 Tbx6b/c/d -1.0130 -17.2024 No No PWM match No PWM match KH2012:KH.C1.1025 NF-X-like -0.6035 -3.8265 -0.3780 -1.6654 No No PWM match No PWM match KH2012:KH.S406.15 Serum response factor -0.6734 -3.8359 -0.5027 -3.2057 Not Analyzed -2.713 -2.396 KH2012:KH.C4.84 Otx -1.2412 -14.7210 No 1.03 3.2655 KH2012:KH.C1.661 MAD -0.6164 -3.9947 -0.4783 -1.0433 No No PWM match No PWM match KH2012:KH.C3.230 Smad6/7 -0.6892 -4.5477 0.1037 0.3979 Not Analyzed No PWM match No PWM match KH2012:KH.C11.485 Irx-B -0.6444 -3.3356 0.2920 4.8112 No No PWM Hits No PWM Hits KH2012:KH.S215.4 Lhx3 -0.7533 -3.1962 0.2866 1.0258 Not Analyzed -0.3545 8.5955

KH2012:KH.C13.138 CREB/ATF-d -0.6577 -4.3059 -0.6871 -2.7219 No No PWM match No PWM match KH2012:KH.C3.312 E(spl)/hairy-b -0.7883 -4.7748 0.3083 0.5831 Not Analyzed -2.384 No PWM Hits KH2012:KH.L99.12 SREBP -0.7011 -5.1988 -0.9217 -2.9877 No No PWM match No PWM match KH2012:KH.C8.247 ELK -0.8217 -5.5320 0.6453 0.8153 Not Analyzed 4.098 9.539 JASPAR 2020 Max Z-score Max Z-score KH2012:KH.L41.39 Orphan bHLH-4 -0.7187 -3.3780 -0.4214 -1.3573 No No PWM match No PWM match KH2012:KH.C3.651 IRF-like5 -0.8498 -5.3223 -0.9412 -4.1103 Not Analyzed No PWM match No PWM match PWM cluster in cluster in cluster KH2012:KH.C8.143 PPAR -0.7416 -3.6285 -0.5929 -1.1503 No No PWM Hits 3.7255 KH2012:KH.C5.362 CBF1 interacting corepressor-like -0.8666 -5.3489 -0.8936 -2.3739 Not Analyzed No PWM match No PWM match KH2012:KH.C1.725 NF-E2 -0.8563 -3.8337 -0.8023 -2.4196 No -2.0105 6.0295 KH2012:KH.C14.520 Orphan Fox-1 -0.8953 -7.6114 0.3655 0.4809 Not Analyzed 1.6485 10.4105 E2F7 22.25 KH2012:KH.C7.782 POU-like -0.9096 -6.9654 -0.9355 -3.9516 No No PWM match No PWM match KH2012:KH.L153.85 Zinc Finger (C2H2)-8 -0.8976 -4.6064 -1.0038 -2.9973 Not Analyzed 2.496 2.496 ARNT2 21.33 USF2 KH2012:KH.C3.312 E(spl)/hairy-b -1.0442 -5.8260 -0.0998 -0.6273 No 5.513 No PWM Hits KH2012:KH.S899.4 BTF3 -1.0136 -8.5389 -0.0535 -0.3244 Not Analyzed No PWM match No PWM match SP3 18.11 KLF6 KH2012:KH.C3.348 E12/E47 -1.2148 -7.3855 -0.4435 -1.2849 No 2.462 5.765 KH2012:KH.C3.348 E12/E47 -1.0722 -8.1697 0.1519 0.3160 Not Analyzed 7.58 14.41 CTCF 17.65 CTCF KH2012:KH.C7.111 Transcription initiation protein SPT4 homolog -1.2544 -6.9887 -1.4263 -4.7463 No No PWM match No PWM match KH2012:KH.L9.33 E(Y)2 -1.1610 -4.9337 -0.6381 -3.6026 Not Analyzed No PWM match No PWM match Esrrg 17.31 NR2F1 KH2012:KH.C14.520 Orphan Fox-1 -1.4828 -6.8471 -0.3758 -0.7197 No 0.107 9.7745 KH2012:KH.L4.17 Zinc Finger (C2H2)-18 -1.1714 -9.6645 0.0811 0.1882 Not Analyzed -2.872 -2.872 TFAP2B 15.42 TFAP2C KH2012:KH.C8.247 ELK -1.7536 -9.6904 -0.0702 -0.4717 No 2.6735 6.755 KH2012:KH.C11.485 Irx-B -1.3000 -8.5752 -0.1296 -0.3979 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.S215.4 Lhx3 -1.8932 -8.0218 -0.1092 -0.6273 No -0.794 9.694 KH2012:KH.C3.17 ROR -1.5194 -10.0704 -0.7379 -1.8978 Not Analyzed 3.4095 10.349 KH2012:KH.C3.751 Snail -2.2650 -9.3160 -0.0403 -0.2866 No -1.068 5.765 KH2012:KH.C14.307 MyoD -1.6190 -8.7507 0.0994 0.5831 Not Analyzed -2.098 No PWM Hits KH2012:KH.C4.84 Otx -2.7891 -10.2320 0.4197 3.1142 No 1.326 3.2035 KH2012:KH.C14.377 Otp -1.6868 -11.3042 0.5413 1.0258 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.S654.3 Tbx6b/c/d -2.1419 -13.8741 0.0562 0.5831 Not Analyzed No PWM match No PWM match KH2012:KH.C3.751 Snail -2.2347 -14.5871 0.6866 1.4370 Not Analyzed 9.598 14.41 KH2012:KH.C4.84 Otx -2.7103 -16.3511 0.1251 0.5718 Not Analyzed -6.3165 1.1615 JASPAR 2020 Max Z-score Max Z-score KH2012:KH.C3.100 Mesp -2.9892 -16.2643 0.2373 0.5831 Not Analyzed No PWM match No PWM match PWM cluster in cluster in cluster KH2012:KH.S423.6 SMYD1 -3.1946 -14.0670 0.4753 1.0258 Not Analyzed No PWM match No PWM match Nr2f6 41.60 NR1H2::RXRA Esrrg 16.43 NR2F1

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster NR3C1 22.69 Ar

B7.5 B7.5 Trunk Ventral Cells KH2012 TF common name Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C4.84 Otx 1.2412 14.7210 Yes -0.7735 4.672 KH2012:KH.C4.84 Otx 2.7891 10.2320 1.9676 35.9834 Yes -2.832 8.1165 KH2012:KH.S423.6 SMYD1 3.1946 14.0670 3.6216 28.1727 Not Analyzed No PWM match No PWM match KH2012:KH.S654.3 Tbx6b/c/d 1.0130 17.2024 Yes No PWM match No PWM match KH2012:KH.S654.3 Tbx6b/c/d 2.4514 9.7784 1.4384 26.6766 Yes No PWM match No PWM match KH2012:KH.C3.100 Mesp 2.9892 16.2643 1.1681 12.5425 Not Analyzed No PWM match No PWM match KH2012:KH.C3.751 Snail 0.7634 8.3360 No -1.8875 12.241 KH2012:KH.C3.751 Snail 2.2650 9.3160 1.4613 28.7829 Yes 2.399 13.799 KH2012:KH.C4.84 Otx 2.7103 16.3511 0.0463 0.0905 Not Analyzed 12.459 16.8505 KH2012:KH.S816.1 ZicL 0.7631 11.8046 Yes 14.6085 14.6085 KH2012:KH.C3.100 Mesp 2.0584 8.4379 2.0584 52.8109 Yes No PWM match No PWM match KH2012:KH.C3.751 Snail 2.2347 14.5871 0.6564 7.0890 Not Analyzed -15.9005 9.6145 KH2012:KH.C3.312 E(spl)/hairy-b 0.6040 6.9172 No 1.0115 No PWM Hits KH2012:KH.S215.4 Lhx3 1.8932 8.0218 1.5644 34.4286 Yes 2.7255 18.0585 KH2012:KH.S654.3 Tbx6b/c/d 2.1419 13.8741 -0.2533 -1.6977 Not Analyzed No PWM match No PWM match KH2012:KH.C7.157 Emc 0.5819 4.5001 No No PWM match No PWM match KH2012:KH.C8.247 ELK 1.7536 9.6904 1.4083 33.6194 No -4.8805 4.01 KH2012:KH.C14.377 Otp 1.6868 11.3042 1.7181 21.1322 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.C9.892 RXR 0.4978 2.6395 No -2.545 3.2755 KH2012:KH.S816.1 ZicL 1.6048 8.0218 0.8417 15.3930 Yes 0.0629999999999997 7.047 KH2012:KH.C14.307 MyoD 1.6190 8.7507 1.5412 14.0761 Not Analyzed 3.7995 No PWM Hits KH2012:KH.C3.697 Zinc Finger (C2H2)-5 0.4955 4.1111 No 6.7595 6.7595 KH2012:KH.C14.520 Orphan Fox-1 1.4828 6.8471 0.8159 12.5909 Yes -0.1195 10.625 KH2012:KH.C3.17 ROR 1.5194 10.0704 1.3137 13.9179 Not Analyzed -5.6775 7.8995 KH2012:KH.C3.103 RBP1-like 0.4240 8.3677 No No PWM match No PWM match KH2012:KH.C7.111 Transcription initiation protein SPT4 homolog 1.2544 6.9887 -0.0432 -0.3355 No No PWM match No PWM match KH2012:KH.C11.485 Irx-B 1.3000 8.5752 0.5260 2.8422 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.S406.15 Serum response factor 0.4144 2.4656 No 0.897 0.897 KH2012:KH.C3.348 E12/E47 1.2148 7.3855 0.6606 12.8443 Yes -5.2565 13.799 KH2012:KH.L4.17 Zinc Finger (C2H2)-18 1.1714 9.6645 1.4996 22.5594 Not Analyzed 0.246 0.246 KH2012:KH.C1.677 Smcx/SMCY/PLU-1/RBP-2 like 1 0.3871 3.7430 No No PWM match No PWM match KH2012:KH.C3.312 E(spl)/hairy-b 1.0442 5.8260 0.3405 6.3643 No -10.8105 No PWM Hits KH2012:KH.L9.33 E(Y)2 1.1610 4.9337 0.1289 0.4540 Not Analyzed No PWM match No PWM match KH2012:KH.C11.351 NF45 -0.3846 -3.9428 No No PWM match No PWM match KH2012:KH.C7.782 POU-like 0.9096 6.9654 -0.1983 -0.9721 No No PWM match No PWM match KH2012:KH.C3.348 E12/E47 1.0722 8.1697 0.0093 0.1945 Not Analyzed -12.6305 9.6145 KH2012:KH.C1.777 Zinc Finger (C2H2)-33 -0.5126 -6.3127 No 1.043 12.241 KH2012:KH.C1.725 NF-E2 0.8563 3.8337 -0.0644 -0.4245 No 5.7325 12.228 KH2012:KH.S899.4 BTF3 1.0136 8.5389 0.4237 4.9549 Not Analyzed No PWM match No PWM match KH2012:KH.C8.450 Nkx-A -0.7090 -10.5529 No No PWM match No PWM match KH2012:KH.C8.143 PPAR 0.7416 3.6285 0.3052 5.0814 No No PWM Hits -2.394 KH2012:KH.L153.85 Zinc Finger (C2H2)-8 0.8976 4.6064 0.0798 0.5808 Not Analyzed -4.5925 8.2 KH2012:KH.C1.1016 GCNF -0.9014 -11.4726 No No PWM match No PWM match KH2012:KH.L41.39 Orphan bHLH-4 0.7187 3.3780 0.3149 4.0733 No No PWM match No PWM match KH2012:KH.C14.520 Orphan Fox-1 0.8953 7.6114 -0.2220 -1.3408 Not Analyzed -1.8295 3.318 KH2012:KH.C1.727 macho-1 -2.3339 -44.9245 No -1.441 No PWM Hits KH2012:KH.L99.12 SREBP 0.7011 5.1988 -0.4486 -2.3346 No No PWM match No PWM match KH2012:KH.C5.362 CBF1 interacting corepressor-like 0.8666 5.3489 -0.1953 -5.0408 Not Analyzed No PWM match No PWM match KH2012:KH.L8.11 Tbx6a 0.6711 4.9028 0.6438 31.1216 Yes No PWM match No PWM match KH2012:KH.C3.651 IRF-like5 0.8498 5.3223 -0.1981 -2.2365 Not Analyzed No PWM match No PWM match KH2012:KH.C13.138 CREB/ATF-d 0.6577 4.3059 -0.0629 -0.1005 No No PWM match No PWM match KH2012:KH.C8.247 ELK 0.8217 5.5320 -0.2865 -1.9991 Not Analyzed -6.6965 17.4125 KH2012:KH.C11.485 Irx-B 0.6444 3.3356 0.7875 27.7677 No No PWM Hits No PWM Hits KH2012:KH.C3.312 E(spl)/hairy-b 0.7883 4.7748 0.0524 0.6035 Not Analyzed 3.8205 No PWM Hits JASPAR 2020 Max Z-score Max Z-score KH2012:KH.C1.661 MAD 0.6164 3.9947 0.1346 5.6366 No No PWM match No PWM match KH2012:KH.L96.87 Tbx2/3 0.7724 5.3779 0.6143 4.9427 Not Analyzed 19.2645 19.2645 PWM cluster in cluster in cluster KH2012:KH.C1.1025 NF-X-like 0.6035 3.8265 0.1451 1.8728 No No PWM match No PWM match KH2012:KH.S215.4 Lhx3 0.7533 3.1962 -0.8533 -10.4516 Not Analyzed 1.194 15.4375 KH2012:KH.C1.159 E(spl)/hairy-a 0.5868 3.3430 0.4868 15.6367 No -10.8105 No PWM Hits KH2012:KH.C3.230 Smad6/7 0.6892 4.5477 0.1350 0.1509 Not Analyzed No PWM match No PWM match FOSL2::JUNB_var_2_ 18.69 ATF2 KH2012:KH.L122.11 metastasis associated protein 0.5496 3.3639 0.5241 11.4504 No No PWM match No PWM match KH2012:KH.S406.15 Serum response factor 0.6734 3.8359 -0.0718 -3.4095 Not Analyzed 6.3945 10.7665 PDX1 15.99 mix-a KH2012:KH.L87.58 Zinc Finger (C2H2)-4 0.5430 3.8250 -0.0888 -0.8332 No No PWM Hits No PWM Hits KH2012:KH.C5.130 Zinc Finger (C2H2)-27 0.6704 3.0017 0.0457 0.3868 Not Analyzed 4.6535 10.2335 KH2012:KH.C10.49 Bcl3 0.5406 4.0795 -0.0723 -3.1216 No No PWM match No PWM match KH2012:KH.C8.920 TR2/4 0.6336 3.3469 0.0896 0.8199 Not Analyzed 1.717 13.042 KH2012:KH.S899.4 BTF3 0.5364 3.2760 -0.3558 -4.5588 No No PWM match No PWM match KH2012:KH.L53.12 Zinc Finger (C2H2)-15 0.6325 4.4759 -0.1306 -1.2858 Not Analyzed -4.01 3.1855 KH2012:KH.C3.402 IRF-like7 0.5208 3.1146 0.0842 2.3948 No No PWM match No PWM match KH2012:KH.C1.661 MAD 0.6263 4.3790 0.0604 0.0000 Not Analyzed No PWM match No PWM match KH2012:KH.C14.377 Otp 0.5100 3.1146 0.5100 22.4305 No No PWM Hits No PWM Hits KH2012:KH.L165.2 HIV TAT specific factor 1 (HTATSF1) 0.6164 5.6263 0.6068 7.9715 Not Analyzed No PWM match No PWM match KH2012:KH.L18.112 Zinc finger (PHD/NFX, DDT) 0.5084 3.0771 0.0871 1.8866 No No PWM match No PWM match KH2012:KH.L128.12 Mnx 0.6022 3.8015 0.9444 10.4491 Not Analyzed 4.981 15.4375 KH2012:KH.L20.34 Mnt-like 0.4375 3.1146 -0.0225 -3.0146 No No PWM match No PWM match KH2012:KH.C11.450 CBF 0.5682 3.9961 0.3631 2.8703 Not Analyzed No PWM match No PWM match KH2012:KH.C4.810 HSF -0.4277 -3.0314 0.1753 3.7531 No No PWM match No PWM match KH2012:KH.C1.275 STAT-b 0.5620 3.4069 0.0426 0.7469 Not Analyzed No PWM match No PWM match KH2012:KH.S1159.1 Fli/ERG4 -0.5398 -4.4990 -0.0428 -0.1360 No No PWM match No PWM match KH2012:KH.L60.12 transcription factor Dp-1 0.5570 4.1963 0.1499 0.2806 Not Analyzed No PWM match No PWM match KH2012:KH.C7.334 Gli -0.8588 -5.6709 -0.0308 -0.4593 No 7.047 7.047 KH2012:KH.C6.223 E2F4/5 0.4817 3.2690 -0.1254 -4.4922 Not Analyzed 12.356 19.2675 KH2012:KH.C10.92 Baf57 -1.1650 -16.5951 0.0316 1.1374 No No PWM match No PWM match KH2012:KH.S437.3 Zinc Finger (C2H2)-10 0.4622 3.1992 -0.1825 -2.1134 Not Analyzed 11.831 11.831 KH2012:KH.C1.1016 GCNF -1.3337 -4.9628 -0.0398 -1.9155 No No PWM match No PWM match KH2012:KH.C8.450 Nkx-A -1.1482 -4.7606 -0.1131 -2.0354 Not Analyzed No PWM match No PWM match KH2012:KH.C1.777 Zinc Finger (C2H2)-33 -1.9082 -10.1472 0.2260 10.7351 No -9.3385 13.799 KH2012:KH.C1.1016 GCNF -2.1354 -10.9785 0.3242 0.4938 Not Analyzed No PWM match No PWM match KH2012:KH.C1.727 macho-1 -3.8125 -14.1546 -0.1457 -0.4449 No 5.8695 No PWM Hits KH2012:KH.C1.727 macho-1 -3.4617 -18.5699 -0.1662 -3.1393 Not Analyzed 0.809 No PWM Hits

JASPAR 2020 Max Z-score Max Z-score JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster PWM cluster in cluster in cluster SOX8 37.05 Sox11 ARNT2 40.28 CREB3 SRF 29.18 SRF IRF8 39.64 IRF9 EWSR1-FLI1 23.48 ZNF24 Rhox11 22.82 Rhox11 SP3 20.71 SP2 E2F7 19.27 E2F1 ZNF384 19.98 ZNF384 TBX21 19.26 TBX2 E2F7 18.62 E2F8 Hmx1 18.70 Alx1 IRF8 18.11 Stat2 ELK3 17.41 ELF3 PDX1 18.06 Dlx1 PITX3 16.85 GSC PRDM1 17.40 PRDM1 FOSL2::JUNB_var_2_ 16.82 CREB1 SCRT1 16.51 SCRT1 ZNF135 16.36 ZNF135 TBX21 15.93 TBX18 RUNX1 16.16 RUNX1 ZBTB7B 15.02 ZBTB7B PDX1 15.44 PRRX2 TBX19 15.05 TBXT

B7.8 B7.8 Muscle B7.8 Muscle KH2012 TF common name Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C14.307 MyoD 0.9594 37.5999 Yes 13.104 No PWM Hits KH2012:KH.S423.6 SMYD1 3.2247 34.9451 2.9139 44.0922 Yes No PWM match No PWM match KH2012:KH.S423.6 SMYD1 4.7990 31.7939 2.0492 43.9645 Not Analyzed No PWM match No PWM match KH2012:KH.S654.3 Tbx6b/c/d 0.4527 8.1693 No No PWM match No PWM match KH2012:KH.C14.307 MyoD 1.8165 31.1811 0.8683 17.2457 Yes 10.8995 No PWM Hits KH2012:KH.S654.3 Tbx6b/c/d 2.5740 31.2019 0.8497 21.5070 Not Analyzed No PWM match No PWM match KH2012:KH.C14.377 Otp 0.4393 17.1817 Yes No PWM Hits No PWM Hits KH2012:KH.C14.377 Otp 1.8102 34.7566 1.4610 37.1476 Yes No PWM Hits No PWM Hits KH2012:KH.C14.307 MyoD 2.5162 30.7207 0.6483 13.1393 Not Analyzed 37.9995 No PWM Hits KH2012:KH.C3.773 Ci-mT 0.4344 5.5269 No No PWM match No PWM match KH2012:KH.S654.3 Tbx6b/c/d 1.4120 25.8127 0.9621 21.2189 Yes No PWM match No PWM match KH2012:KH.C14.377 Otp 2.4295 30.0668 0.5988 8.0539 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.S423.6 SMYD1 0.4326 17.7084 No No PWM match No PWM match KH2012:KH.C3.773 Ci-mT 0.6485 8.8627 -0.6001 -7.5740 No No PWM match No PWM match KH2012:KH.C3.751 Snail 1.8771 29.3892 0.8389 26.4077 Not Analyzed -6.288 43.013 KH2012:KH.C3.751 Snail 0.4063 5.4537 No 1.384 22.9865 KH2012:KH.L4.17 Zinc Finger (C2H2)-18 0.5897 7.0645 0.6811 10.1563 No 26.398 26.398 KH2012:KH.L128.12 Mnx 1.8086 22.6402 1.7138 34.1801 Not Analyzed -3.069 10.0855 KH2012:KH.C14.520 Orphan Fox-1 0.3723 8.0381 No -8.706 5.5425 KH2012:KH.C1.661 MAD 0.4960 6.9400 0.1812 2.4153 No No PWM match No PWM match KH2012:KH.C9.717 FoxH-a 1.6823 27.3402 1.6902 46.0278 Not Analyzed -0.2325 9.0225 KH2012:KH.C8.247 ELK -0.3641 -4.0482 No 5.06 6.494 KH2012:KH.C1.159 E(spl)/hairy-a -0.4831 -8.7417 -0.0408 -0.2433 No -4.0785 No PWM Hits KH2012:KH.C1.264 Y-box protein1/2/3 1.6227 27.6601 1.6293 40.6028 Not Analyzed No PWM match No PWM match KH2012:KH.C5.416 TWIST-like-1a/b -0.4680 -7.3404 No No PWM match No PWM match KH2012:KH.C11.314 Fos -0.7166 -17.7417 0.2839 8.2692 No -1 4.6555 KH2012:KH.C3.17 ROR 1.4213 26.4261 1.4152 37.6529 Not Analyzed 8.1715 14.5365 KH2012:KH.C11.485 Irx-B -0.5389 -5.5026 No No PWM Hits No PWM Hits KH2012:KH.C3.230 Smad6/7 -0.7583 -16.6623 0.1663 5.8646 No No PWM match No PWM match KH2012:KH.C9.580 RAR 1.1272 17.2936 0.9888 22.3853 Not Analyzed 8.049 10.8795 KH2012:KH.C10.148 Fli/ERG3 -0.7975 -24.0451 -0.0333 -0.4136 No -16.8215 2.857 KH2012:KH.L96.87 Tbx2/3 1.1195 17.0794 0.7909 14.5944 Not Analyzed 20.029 27.6755 KH2012:KH.C11.485 Irx-B -1.0304 -16.9220 0.5630 3.1442 No No PWM Hits No PWM Hits KH2012:KH.L4.17 Zinc Finger (C2H2)-18 0.7913 10.9101 0.8734 18.9249 Not Analyzed 5.45 5.45 KH2012:KH.C8.247 ELK -1.6919 -29.5361 0.0347 1.7665 No -8.591 2.857 KH2012:KH.C2.725 Su(H)/RBP-J 0.6457 6.1362 0.5481 6.1144 Not Analyzed No PWM Hits No PWM Hits JASPAR 2020 Max Z-score Max Z-score KH2012:KH.C5.416 TWIST-like-1a/b -2.0931 -40.2886 0.0160 1.4608 No No PWM match No PWM match KH2012:KH.C3.84 HNF4 0.6017 5.8451 0.2871 2.0655 Not Analyzed -5.6285 4.044 PWM cluster in cluster in cluster KH2012:KH.C3.312 E(spl)/hairy-b 0.5831 5.6513 0.5116 6.4250 Not Analyzed -0.865 No PWM Hits KH2012:KH.C10.174 meis 0.5812 7.2732 0.5865 14.8889 Not Analyzed 9.1645 11.4825 IRF8 27.91 STAT1::STAT2 KH2012:KH.C3.348 E12/E47 0.5347 7.2929 0.3896 7.5347 Not Analyzed 16.355 43.013 FOS::JUNB 23.63 BACH2 KH2012:KH.C1.669 Zinc Finger (C2H2)-25 0.5102 4.9848 0.6262 9.7246 Not Analyzed 0.707 0.707 TBX21 23.55 EOMES JASPAR 2020 Max Z-score Max Z-score KH2012:KH.C4.83 HIF 0.4990 4.2125 0.5269 6.3760 Not Analyzed No PWM match No PWM match MAFG 23.11 MAFF PWM cluster in cluster in cluster KH2012:KH.S899.4 BTF3 0.4920 10.5191 0.6591 22.5428 Not Analyzed No PWM match No PWM match Rarg 23.07 NR1D1 RREB1 26.40 RREB1 KH2012:KH.C1.661 MAD 0.4398 5.7655 0.3188 3.9673 Not Analyzed No PWM match No PWM match BHLHA15_var_2_ 22.99 MYOD1 Nr2f6 20.27 Rxra KH2012:KH.L13.24 FoxN2/3 0.4259 5.0303 0.5245 8.3652 Not Analyzed -9.6185 0.1655 HSF2 22.76 HSF1 TBX21 18.01 TBX2 KH2012:KH.C11.314 Fos -0.4077 -9.2806 -0.1551 -3.1659 Not Analyzed -1.789 6.1225 PITX3 22.18 FOXH1 ZSCAN4 17.81 ZSCAN4 KH2012:KH.C7.111 Transcription initiation protein SPT4 homolog -0.4447 -5.8039 -0.6107 -10.5912 Not Analyzed No PWM match No PWM match Stat5a::Stat5b 20.42 STAT1 BHLHA15_var_2_ 16.13 TCF3 KH2012:KH.C1.777 Zinc Finger (C2H2)-33 -0.4725 -6.3145 -0.1573 -4.0765 Not Analyzed 2.749 43.013 PHOX2A 17.35 DUXA KH2012:KH.C10.245 AF10like -0.4878 -4.4252 -0.3392 -7.4527 Not Analyzed No PWM match No PWM match PBX3 17.10 PKNOX1 KH2012:KH.C5.90 core-binding factor, β subunit -0.4899 -6.8066 -0.3252 -7.6202 Not Analyzed No PWM match No PWM match GLIS2 16.29 ZIC4 KH2012:KH.C1.516 HMG20 -0.4925 -6.0098 -0.4817 -7.6640 Not Analyzed No PWM match No PWM match Esrrg 15.09 NR2C1 KH2012:KH.C14.306 IRF-like 2 -0.4945 -6.6127 -0.5153 -10.2559 Not Analyzed No PWM match No PWM match KH2012:KH.C11.620 ubiquitin-like, containing PHD and RING finger domains, 1 -0.4974 -12.4332 -0.6748 -25.5616 Not Analyzed No PWM match No PWM match KH2012:KH.C11.313 FoxA-a -0.4992 -9.2300 -0.0307 -1.5042 Not Analyzed -5.474 No PWM Hits KH2012:KH.S1482.3 NFRKB -0.5420 -6.3952 -0.3494 -6.9234 Not Analyzed No PWM match No PWM match KH2012:KH.L41.71 Zinc Finger (C2H2)-32 -0.5518 -6.1425 -0.6091 -14.2108 Not Analyzed No PWM match No PWM match KH2012:KH.C14.178 HMG1/2 -0.5521 -14.2229 -0.1379 -1.9025 Not Analyzed No PWM match No PWM match KH2012:KH.C8.162 Zinc Finger (C2H2)-21 -0.5690 -3.3104 -0.2458 -4.5916 Not Analyzed -7.15 -4.162 KH2012:KH.C8.247 ELK -0.6276 -7.1980 0.1056 0.0682 Not Analyzed 1.713 9.713 KH2012:KH.C14.278 Zinc Finger (C2H2)-34 -0.6586 -7.8820 -0.9761 -27.8768 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.C2.822 E2F1/2/3/6 -0.6931 -6.6567 -0.7839 -15.0787 Not Analyzed No PWM match No PWM match KH2012:KH.C2.573 Smad1/5 -0.7094 -12.3360 -0.7288 -22.3578 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.C9.892 RXR -0.7664 -10.5124 -0.2542 -5.7793 Not Analyzed -4.477 9.2285 KH2012:KH.C10.148 Fli/ERG3 -0.8835 -16.7505 -0.0366 -2.0261 Not Analyzed -3.674 9.713 KH2012:KH.C4.84 Otx -1.1448 -8.9319 -1.6302 -36.9315 Not Analyzed 1.3495 9.0225 KH2012:KH.C4.182 Zinc Finger (C3H) -1.3523 -25.5426 0.0045 0.3097 Not Analyzed No PWM match No PWM match KH2012:KH.C5.416 TWIST-like-1a/b -2.1980 -32.7559 -0.0160 -1.5042 Not Analyzed No PWM match No PWM match

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster BHLHA15_var_2_ 43.01 MYOG TBX21 27.68 TBX18 Rhox11 23.08 ZNF341 FOSL2::JUNB_var_2_ 20.96 CREM Zic1::Zic2 20.56 ZNF317 TFAP2B 18.90 EBF1 Gmeb1 17.13 Gmeb1 MAFG 16.88 Mafb E2F7 16.52 E2F1 TBX19 15.91 TBX19

B7.7 B7.7 B7.7 Mesenchyme KH2012 TF common name Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster KH2012 TF common name Log2FC -Log(pvalue) Log2FC -Log(pvalue) DE in Imai Matched PWM PWM Cluster gene model Sibling Cluster Sibling Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score gene model Sibling Cluster Sibling Cluster Parent Cluster Parent Cluster z-score z-score KH2012:KH.C11.485 Irx-B 0.5389 5.5026 No No PWM Hits No PWM Hits KH2012:KH.C5.416 TWIST-like-1a/b 2.0931 40.2886 1.6411 37.1325 Yes No PWM match No PWM match KH2012:KH.C5.416 TWIST-like-1a/b 2.1980 32.7559 0.0889 0.5182 Not Analyzed No PWM match No PWM match KH2012:KH.C5.416 TWIST-like-1a/b 0.4680 7.3404 Yes No PWM match No PWM match KH2012:KH.C8.247 ELK 1.6919 29.5361 1.3625 30.0256 Yes 14.4105 28.446 KH2012:KH.C5.202 TWIST-like-2 1.6145 24.1943 0.8218 2.0460 Not Analyzed No PWM match No PWM match KH2012:KH.C8.247 ELK 0.3641 4.0482 Yes -1.2635 12.8905 KH2012:KH.C11.485 Irx-B 1.0304 16.9220 1.0546 24.3838 Yes No PWM Hits No PWM Hits KH2012:KH.C4.182 Zinc Finger (C3H) 1.3523 25.5426 1.2063 15.8774 Not Analyzed No PWM match No PWM match KH2012:KH.C14.520 Orphan Fox-1 -0.3723 -8.0381 No 6.4535 10.075 KH2012:KH.C10.148 Fli/ERG3 0.7975 24.0451 0.7271 29.6104 Yes 28.099 28.446 KH2012:KH.C4.84 Otx 1.1448 8.9319 -0.8223 -9.9984 Not Analyzed -1.8125 5.5 KH2012:KH.C3.751 Snail -0.4063 -5.4537 No -0.8895 7.096 KH2012:KH.C4.539 Fli/ERG1 0.7936 35.1674 0.7878 57.7429 Yes 25.228 28.446 KH2012:KH.C4.539 Fli/ERG1 1.0964 22.8809 0.3028 0.9166 Not Analyzed 0.591 15.3215 KH2012:KH.S423.6 SMYD1 -0.4326 -17.7084 No No PWM match No PWM match KH2012:KH.C5.202 TWIST-like-2 0.7927 31.8207 0.7927 55.1222 No No PWM match No PWM match KH2012:KH.C10.148 Fli/ERG3 0.8835 16.7505 0.0494 0.4619 Not Analyzed 4.3845 15.3215 KH2012:KH.C3.773 Ci-mT -0.4344 -5.5269 No No PWM match No PWM match KH2012:KH.C3.230 Smad6/7 0.7583 16.6623 0.8915 26.6384 Yes No PWM match No PWM match KH2012:KH.C9.892 RXR 0.7664 10.5124 0.3773 1.0037 Not Analyzed 6.332 7.7465 KH2012:KH.C14.377 Otp -0.4393 -17.1817 No No PWM Hits No PWM Hits KH2012:KH.C11.314 Fos 0.7166 17.7417 0.9244 46.1530 Yes 1.2165 15.408 KH2012:KH.C2.573 Smad1/5 0.7094 12.3360 -0.1810 -1.3154 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.S654.3 Tbx6b/c/d -0.4527 -8.1693 No No PWM match No PWM match KH2012:KH.C1.159 E(spl)/hairy-a 0.4831 8.7417 0.5180 17.9326 No 5.2155 No PWM Hits KH2012:KH.C2.822 E2F1/2/3/6 0.6931 6.6567 -0.1546 -2.5026 Not Analyzed No PWM match No PWM match KH2012:KH.C14.307 MyoD -0.9594 -37.5999 No -6.11 No PWM Hits KH2012:KH.C1.661 MAD -0.4960 -6.9400 -0.3737 -2.9542 No No PWM match No PWM match KH2012:KH.C14.278 Zinc Finger (C2H2)-34 0.6586 7.8820 -0.2227 -2.4018 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.L4.17 Zinc Finger (C2H2)-18 -0.5897 -7.0645 0.1416 1.7066 No -14.8955 -14.8955 KH2012:KH.C8.247 ELK 0.6276 7.1980 -0.9587 -13.7501 Not Analyzed -2.5845 15.3215 KH2012:KH.C3.773 Ci-mT -0.6485 -8.8627 -0.8142 -9.7134 No No PWM match No PWM match KH2012:KH.C8.162 Zinc Finger (C2H2)-21 0.5690 3.3104 0.2830 0.7482 Not Analyzed 9.5095 19.4165 KH2012:KH.S654.3 Tbx6b/c/d -1.4120 -25.8127 0.0028 1.2203 No No PWM match No PWM match KH2012:KH.C14.178 HMG1/2 0.5521 14.2229 0.4377 9.2934 Not Analyzed No PWM match No PWM match JASPAR 2020 Max Z-score Max Z-score KH2012:KH.C14.377 Otp -1.8102 -34.7566 0.0901 11.2909 No No PWM Hits No PWM Hits KH2012:KH.L41.71 Zinc Finger (C2H2)-32 0.5518 6.1425 -0.0437 -1.0281 Not Analyzed No PWM match No PWM match PWM cluster in cluster in cluster KH2012:KH.C14.307 MyoD -1.8165 -31.1811 0.0111 0.0000 No -12.0585 No PWM Hits KH2012:KH.S1482.3 NFRKB 0.5420 6.3952 0.2052 0.7557 Not Analyzed No PWM match No PWM match KH2012:KH.S423.6 SMYD1 -3.2247 -34.9451 0.1219 7.5358 No No PWM match No PWM match KH2012:KH.C11.313 FoxA-a 0.4992 9.2300 0.4992 6.5468 Not Analyzed 7.9015 No PWM Hits PAX1 43.70 PAX9 KH2012:KH.C11.620 ubiquitin-like, containing PHD and RING finger domains, 1 0.4974 12.4332 -0.1329 -1.2240 Not Analyzed No PWM match No PWM match NFKB2 21.58 NFKB2 KH2012:KH.C14.306 IRF-like 2 0.4945 6.6127 0.2271 2.9541 Not Analyzed No PWM match No PWM match KH2012:KH.C1.516 HMG20 0.4925 6.0098 0.0039 1.4065 Not Analyzed No PWM match No PWM match JASPAR 2020 Max Z-score Max Z-score KH2012:KH.C5.90 core-binding factor, β subunit 0.4899 6.8066 0.1876 0.6022 Not Analyzed No PWM match No PWM match PWM cluster in cluster in cluster KH2012:KH.C10.245 AF10like 0.4878 4.4252 -0.0268 -2.0467 Not Analyzed No PWM match No PWM match KH2012:KH.C1.777 Zinc Finger (C2H2)-33 0.4725 6.3145 0.1443 0.9415 Not Analyzed -3.1015 14.012 ELK3 28.45 ETV5 KH2012:KH.C7.111 Transcription initiation protein SPT4 homolog 0.4447 5.8039 -0.2948 -3.7450 Not Analyzed No PWM match No PWM match MAFG 25.80 MAFG KH2012:KH.C11.314 Fos 0.4077 9.2806 -0.4639 -6.8910 Not Analyzed 2.759 26.2875 YY1 21.08 YY1 KH2012:KH.L13.24 FoxN2/3 -0.4259 -5.0303 0.0024 0.2426 Not Analyzed 13.6605 23.455 ESR1 21.04 ESR2 KH2012:KH.C1.661 MAD -0.4398 -5.7655 0.3750 2.4681 Not Analyzed No PWM match No PWM match Stat5a::Stat5b 20.23 STAT1 KH2012:KH.S899.4 BTF3 -0.4920 -10.5191 0.2247 3.7262 Not Analyzed No PWM match No PWM match POU3F1 19.61 Pou5f1:: KH2012:KH.C4.83 HIF -0.4990 -4.2125 -0.1885 -4.4291 Not Analyzed No PWM match No PWM match PAX1 19.46 PAX9 KH2012:KH.C1.669 Zinc Finger (C2H2)-25 -0.5102 -4.9848 0.0882 1.1067 Not Analyzed -0.1745 -0.1745 ZBTB32 19.12 ZBTB32 KH2012:KH.C3.348 E12/E47 -0.5347 -7.2929 0.0317 0.1311 Not Analyzed -17.381 14.012 SMAD3 18.38 ZSCAN29 KH2012:KH.C10.174 meis -0.5812 -7.2732 -0.0076 0.0000 Not Analyzed -11.9145 -9.5165 GCM2 16.89 CENPB KH2012:KH.C3.312 E(spl)/hairy-b -0.5831 -5.6513 0.1914 0.0615 Not Analyzed 0.376000000000001 No PWM Hits PRDM1 16.88 PRDM1 KH2012:KH.C3.84 HNF4 -0.6017 -5.8451 -0.2491 -3.1790 Not Analyzed 8.558 8.558 PITX3 16.06 Dmbx1 KH2012:KH.C2.725 Su(H)/RBP-J -0.6457 -6.1362 -0.0950 -3.4983 Not Analyzed No PWM Hits No PWM Hits OVOL2 15.87 OVOL2 KH2012:KH.L4.17 Zinc Finger (C2H2)-18 -0.7913 -10.9101 0.6718 4.7141 Not Analyzed -9.194 -9.194 FOS::JUNB 15.41 MAF KH2012:KH.L96.87 Tbx2/3 -1.1195 -17.0794 -0.3775 -6.2092 Not Analyzed -19.9575 -3.8275 KH2012:KH.C9.580 RAR -1.1272 -17.2936 -0.1266 -0.6298 Not Analyzed -6.676 -6.3715 KH2012:KH.C3.17 ROR -1.4213 -26.4261 0.2852 2.1324 Not Analyzed -8.2505 3.204 KH2012:KH.C1.264 Y-box protein1/2/3 -1.6227 -27.6601 0.2589 1.5644 Not Analyzed No PWM match No PWM match KH2012:KH.C9.717 FoxH-a -1.6823 -27.3402 0.0079 1.1006 Not Analyzed 1.2615 5.5 KH2012:KH.L128.12 Mnx -1.8086 -22.6402 0.2260 5.1627 Not Analyzed 5.597 24.3725 KH2012:KH.C3.751 Snail -1.8771 -29.3892 -0.7865 -10.8241 Not Analyzed 8.2835 14.012 KH2012:KH.C14.377 Otp -2.4295 -30.0668 -0.0205 -2.8474 Not Analyzed No PWM Hits No PWM Hits KH2012:KH.C14.307 MyoD -2.5162 -30.7207 -0.0514 -1.1006 Not Analyzed -36.661 No PWM Hits KH2012:KH.S654.3 Tbx6b/c/d -2.5740 -31.2019 -0.3122 -5.2219 Not Analyzed No PWM match No PWM match KH2012:KH.S423.6 SMYD1 -4.7990 -31.7939 0.4749 1.8670 Not Analyzed No PWM match No PWM match

JASPAR 2020 Max Z-score Max Z-score PWM cluster in cluster in cluster ZNF384 26.77 ZNF384 FOS::JUNB 26.29 Nfe2l2 SRF 25.50 SRF PDX1 24.37 Dlx1 MEF2D 23.90 MEF2C Foxf1 23.45 FOXI1 Stat5a::Stat5b 21.25 STAT3 POU4F1 21.06 BARX2 NFKB2 19.42 NFKB1 MAFG 19.31 MAFG HOXD10 19.09 HOXB13 POU3F1 17.15 POU5F1 ELK3 15.32 ELF1

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