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 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 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 Zinc Finger (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 E2F2 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