SUPPLEMENTARY RESULTS Supplementary Table 1. Complete listing of transcription factor genes determined to bind differentially in modern human and Neanderthal promoteromes. TF name Wilcoxon stat Wilcoxon pval HGNC ID UniProt ID Description Family LHX3 442284.5 4.83E-38 6595 Q9UBR4 LIM/homeobox protein Lhx3 homeodomain transcription factor(PC00119) PROP1 271411.5 3.18E-35 9455 O75360 Homeobox protein prophet of Pit-1 FOXC1 450055.5 3.71E-33 3800 Q12948 Forkhead box protein C1 winged helix/forkhead transcription factor(PC00246) POU4F3 865739 1.14E-26 9220 Q15319 POU domain, class 4, transcription factor 3 POU4F1 638453.5 2.33E-26 9218 Q01851 POU domain, class 4, transcription factor 1 HOXD8 908880 6.68E-23 5139 P13378 Homeobox protein Hox-D8 FOXB1 510034 9.09E-23 3799 Q99853 Forkhead box protein B1 winged helix/forkhead transcription factor(PC00246) FOXQ1 134647.5 1.03E-21 20951 Q9C009 Forkhead box protein Q1 winged helix/forkhead transcription factor(PC00246) POU4F2 1135242 1.39E-19 9219 Q12837 POU domain, class 4, transcription factor 2 PHOX2A 452784.5 1.45E-19 691 O14813 Paired mesoderm homeobox protein 2A homeodomain transcription factor(PC00119) ARID3B 256994 1.68E-19 14350 Q8IVW6 AT-rich interactive domain-containing protein 3B DNA-binding transcription factor(PC00218) ONECUT2 313241.5 2.12E-19 8139 O95948 One cut domain family member 2 homeodomain transcription factor(PC00119) PHOX2B 510851 9.20E-18 9143 Q99453 Paired mesoderm homeobox protein 2B homeodomain transcription factor(PC00119) PAX7 539656 1.00E-17 8621 P23759 Paired box protein Pax-7 POU3F3 631771 4.21E-17 9216 P20264 POU domain, class 3, transcription factor 3 MAFF 23605 8.03E-17 6780 Q9ULX9 Transcription factor MafF basic leucine zipper transcription factor(PC00056) POU5F1 (POU5F1::SOX2) 43260 8.11E-16 9221 Q01860 POU domain, class 5, transcription factor 1 SOX2 (POU5F1::SOX2) 43260 8.11E-16 11195 P48431 Transcription factor SOX-2 HMG box transcription factor(PC00024) POU2F2 898740 2.16E-15 9213 P09086 POU domain, class 2, transcription factor 2 POU3F1 608911.5 7.17E-15 9214 Q03052 POU domain, class 3, transcription factor 1 ONECUT3 273456 1.17E-14 13399 O60422 One cut domain family member 3 homeodomain transcription factor(PC00119) POU3F2 689576.5 1.92E-14 9215 P20265 POU domain, class 3, transcription factor 2 POU2F1 732151 2.01E-14 9212 P14859 POU domain, class 2, transcription factor 1 FOXC2 296082 1.08E-13 3801 Q99958 Forkhead box protein C2 winged helix/forkhead transcription factor(PC00246) ARID5A 778558 2.08E-13 17361 Q03989 AT-rich interactive domain-containing protein 5A transcription cofactor(PC00217) ONECUT1 131454.5 5.31E-12 8138 Q9UBC0 Hepatocyte nuclear factor 6 homeodomain transcription factor(PC00119) ARID3A 47976.5 1.51E-11 3031 Q99856 AT-rich interactive domain-containing protein 3A DNA-binding transcription factor(PC00218) HOXC10 243032.5 2.52E-11 5122 Q9NYD6 Homeobox protein Hox-C10 CUX1 586 4.24E-11 2557 P39880 Homeobox protein cut-like 1 homeodomain transcription factor(PC00119) POU1F1 1122196 4.30E-11 9210 P28069 Pituitary-specific positive transcription factor 1 POU5F1B 488691 2.07E-09 9223 Q06416 Putative POU domain, class 5, transcription factor 1B MEF2D 437577.5 2.26E-09 6997 Q14814 Myocyte-specific enhancer factor 2D MADS box transcription factor(PC00250) MEF2A 441549 2.41E-09 6993 Q02078 Myocyte-specific enhancer factor 2A MADS box transcription factor(PC00250) NKX2-5 773 7.84E-09 2488 P52952 Homeobox protein Nkx-2.5 homeodomain transcription factor(PC00119) TBX19 4898.5 9.31E-09 11596 O60806 T-box transcription factor TBX19 Rel homology transcription factor(PC00252) LIN54 10569.5 1.05E-08 25397 Q6MZP7 Protein lin-54 homolog PAX3 224681 1.12E-08 8617 P23760 Paired box protein Pax-3 IRF1 4225 1.31E-08 6116 P10914 Interferon regulatory factor 1 winged helix/forkhead transcription factor(PC00246) MECOM 15265.5 3.32E-08 3498 Q03112 Histone-lysine N-methyltransferase MECOM C2H2 zinc finger transcription factor(PC00248) HOXD9 86178.5 3.70E-08 5140 P28356 Homeobox protein Hox-D9 SIX3 3398 5.20E-08 10889 O95343 Homeobox protein SIX3 homeodomain transcription factor(PC00119) MAFK 7199.5 6.53E-08 6782 O60675 Transcription factor MafK basic leucine zipper transcription factor(PC00056) HOXD11 279435.5 1.28E-07 5134 P31277 Homeobox protein Hox-D11 CDX1 172275 2.60E-07 1805 P47902 Homeobox protein CDX-1 homeodomain transcription factor(PC00119) POU3F4 533271 2.67E-07 9217 P49335 POU domain, class 3, transcription factor 4 POU6F1 77984 5.00E-07 9224 Q14863 POU domain, class 6, transcription factor 1 HOXA13 61766 6.26E-07 5102 P31271 Homeobox protein Hox-A13 CEBPA 31 1.23E-06 1833 P49715 CCAAT/enhancer-binding protein alpha basic leucine zipper transcription factor(PC00056) BARHL2 15912 1.48E-06 954 Q9NY43 BarH-like 2 homeobox protein homeodomain transcription factor(PC00119) UNCX -399 3.70E-06 33194 A6NJT0 Homeobox protein unc-4 homolog LMX1B 146337.5 3.95E-06 6654 O60663 LIM homeobox transcription factor 1-beta homeodomain transcription factor(PC00119) MEF2B 542518 4.27E-06 6995 Q02080 Myocyte-specific enhancer factor 2B MADS box transcription factor(PC00250) OTX2 97 5.41E-06 8522 P32243 Homeobox protein OTX2 homeodomain transcription factor(PC00119) HOXD13 90020 1.05E-05 5136 P35453 Homeobox protein Hox-D13 HOXA10 172880 2.30E-05 5100 P31260 Homeobox protein Hox-A10 POU2F3 535473 3.18E-05 19864 Q9UKI9 POU domain, class 2, transcription factor 3 HNF1A 434983 5.38E-05 11621 P20823 Hepatocyte nuclear factor 1-alpha DNA-binding transcription factor(PC00218) HESX1 -684 5.45E-05 4877 Q9UBX0 Homeobox expressed in ES cells 1 HNF1B 294035.5 6.01E-05 11630 P35680 Hepatocyte nuclear factor 1-beta DNA-binding transcription factor(PC00218) MAFG 1054.5 6.43E-05 6781 O15525 Transcription factor MafG basic leucine zipper transcription factor(PC00056) IRF2 557 9.28E-05 6117 P14316 Interferon regulatory factor 2 winged helix/forkhead transcription factor(PC00246) ZNF384 67.5 0.0001402 11955 Q8TF68 Zinc finger protein 384 C2H2 zinc finger transcription factor(PC00248) FOXA2 3489 0.0001624 5022 Q9Y261 Hepatocyte nuclear factor 3-beta winged helix/forkhead transcription factor(PC00246) HMX3 50292 0.0003858 5019 A6NHT5 Homeobox protein HMX3 HMX2 46211 0.0005692 5018 A2RU54 Homeobox protein HMX2 NKX6-2 6468 0.0005991 19321 Q9C056 Homeobox protein Nkx-6.2 homeodomain transcription factor(PC00119) IRF9 1844 0.0007433 6131 Q00978 Interferon regulatory factor 9 winged helix/forkhead transcription factor(PC00246) NR1H3 (NR1H3::RXRA) 685 0.001769 7966 Q13133 Oxysterols receptor LXR-alpha C4 zinc finger nuclear receptor(PC00169) RXRA (NR1H3::RXRA) 685 0.001769 10477 P19793 Retinoic acid receptor RXR-alpha C4 zinc finger nuclear receptor(PC00169) OLIG2 3491.5 0.0018305 9398 Q13516 Oligodendrocyte transcription factor 2 basic helix-loop-helix transcription factor(PC00055) STAT6 -598 0.001918 11368 P42226 Signal transducer and activator of transcription 6 DNA-binding transcription factor(PC00218) MEF2C 351 0.0020757 6996 Q06413 Myocyte-specific enhancer factor 2C MADS box transcription factor(PC00250) FOXF2 29 0.0023199 3810 Q12947 Forkhead box protein F2 VENTX 14790.5 0.0036602 13639 O95231 Homeobox protein VENTX homeodomain transcription factor(PC00119) NR2E1 1400.5 0.0040203 7973 Q9Y466 Nuclear receptor subfamily 2 group E member 1 C4 zinc finger nuclear receptor(PC00169) DUXA 1735 0.0043964 32179 A6NLW8 Double homeobox protein A PITX1 378 0.0045946 9004 P78337 Pituitary homeobox 1 ISL2 132 0.0046249 18524 Q96A47 Insulin gene enhancer protein ISL-2 homeodomain transcription factor(PC00119) FOXD3 102497 0.0046328 3804 Q9UJU5 Forkhead box protein D3 winged helix/forkhead transcription factor(PC00246) TCF7L2 1157.5 0.0051148 11641 Q9NQB0 Transcription factor 7-like 2 EVX1 248 0.0064663 3506 P49640 Homeobox even-skipped homolog protein 1 FOXH1 1345 0.0071219 3814 O75593 Forkhead box protein H1 OTX1 1128.5 0.008041 8521 P32242 Homeobox protein OTX1 homeodomain transcription factor(PC00119) PBX3 -8 0.0082676 8634 P40426 Pre-B-cell leukemia transcription factor 3 homeodomain transcription factor(PC00119) CEBPB 2082 0.0082978 1834 P17676 CCAAT/enhancer-binding protein beta basic leucine zipper transcription factor(PC00056) FOS (FOS::JUN(VAR.2)) -217.5 0.0095211 3796 P01100 Proto-oncogene c-Fos basic leucine zipper transcription factor(PC00056) JUN (FOS::JUN(VAR.2)) -217.5 0.0095211 6204 P05412 Transcription factor AP-1 basic leucine zipper transcription factor(PC00056) HOXB5 7268 0.0096238 5116 P09067 Homeobox protein Hox-B5 homeodomain transcription factor(PC00119) Supplementary Figure 1. Aggregate expression of DB TFs in 100 tissues. FANTOM5 RNA-Seq data was extracted as TPM values and the 100 tissues with highest aggregate expression of the differentially binding TF genes were selected for clustering (Figure 1), resulting in order of tissues shown here. Supplementary Table 2. Ontological terms (Biological Process and Disease) associated with top 100 marker genes of cortical brain cells clusters expressing DB TFs. Supplementary Figure 2. ROC Analysis model performance in the identification of experimentally verified functional TFBSs – random Ensembl transcripts. ROC analysis was performed using experimentally verified functional TFBSs as annotated in the ORegAnno/Pleides/ABS datasets as true positives, where true negatives were random locations in other Ensembl transcripts at the same distance from the TSS as the associated true positive. All ROC curve analyses were performed on TFs which had at least 10 true positives and 50 true negatives per true positive were used for each analysis. Each true positive/negative segment analyzed was 50 nucleotides long, and the highest TFBS score for the relevant dataset(s) was used for each true positive/negative. (A) Barplot of the frequency of experimental data type in the top 20 performing TFBSFootprinter models. (B) Boxplot of ROC scores for TFBSFootprinter and DeepBind for 14 TFs (left). ROC scores were also calculated based on using individual experimental metrics to show how well each contributes to accuracy of the combined model.