TFs Datasets Sequence logos of information models showing cofactor motifs

Top 500 peaks (FOXA motif)

HepG2, Stanford ARID3A (optimal IDR thresholded) Top 5000 peaks (FOXA motif)

All 14818 peaks (IRF motif)

K562, HMS ATF1 (optimal IDR thresholded)

Top 2500 peaks (SP motif)

H1-hESC, HAIB ATF2 Protocol: v042211.1 (optimal IDR thresholded)

All 1860 peaks (USF motif)

GM12878, HAIB Protocol: PCR1x (SPP obtained from Factorbook)

All 1670 peaks (SP motif) GM12878, HAIB Protocol: PCR1x (optimal IDR thresholded) 1550 peaks (USF motif), after masking the SP motif

All 4803 peaks (SP motif)

H1-hESC, HAIB Protocol: v041610.2 (optimal IDR thresholded) 4697 peaks (USF motif), after masking the SP motif

ATF3 All 3284 peaks (SP motif)

HepG2, HAIB Protocol: v041610.1 (optimal IDR thresholded) 3209 peaks (USF motif), after masking the SP motif All 11098 peaks (SP motif)

K562, HAIB, Replicate 1 Protocol: v041610.1 (raw peaks)

All 1232 peaks (SP motif)

K562, HMS (optimal IDR thresholded) 1210 peaks (USF motif), after masking the SP motif

All 4448 peaks (AP1 motif)

BAF155/ HeLa-S3, Stanford SMARCC1 (SPP obtained from Factorbook)

1342 peaks (AP1 motif), after using masking BAF170/ HeLa-S3, Stanford SMARCC2 (SPP obtained from Factorbook)

All 17809 peaks (IRF motif)

GM12878, HAIB Protocol: PCR1x (optimal IDR thresholded) 17321 peaks (RUNX motif), after masking the IRF motif

BCL11A

All 2513 peaks (SOX2-OCT4 motif)

H1-hESC, HAIB Protocol: PCR1x (optimal IDR thresholded)

All 7707 peaks (AP1 motif), after masking noise

A549, HAIB Protocol: v042211.1 BCL3 Treatment: 0.02% ethanol for 1 hour (optimal IDR thresholded)

Top 500 peaks (SP motif) GM12878, HAIB, Replicate 2 Protocol: v041610.1 (raw peaks)

All 2297 peaks (SP motif)

K562, HAIB, Replicate 1 BCLAF1 Protocol:PCR1x (raw peaks)

All 2362 peaks (SP motif)

K562, HAIB, Replicate 2 Protocol:PCR1x (raw peaks)

All 507 peaks (B-Box motif)

H1-hESC, HMS (optimal IDR thresholded)

BDP1 All 569 peaks (A-Box motif)

K562, HMS (optimal IDR thresholded)

Top 4500 peaks (SP motif) BHLHE32/MI K562, HAIB TF (optimal IDR thresholded)

All 550 peaks (ZBTB33 motif)

GM12878, Stanford (optimal IDR thresholded)

All 1999 peaks (SP motif)

H1-hESC, Stanford (optimal IDR thresholded) Top 1000 peaks (ZBTB33 motif)

All 8081 peaks (SP motif)

BRCA1 Top 500 peaks (ZBTB33 motif) HeLa-S3, Stanford (optimal IDR thresholded)

Top 800 peaks (ZBTB33 motif)

All 1489 peaks (SP motif)

HepG2, Stanford (optimal IDR thresholded) Top 800 peaks (ZBTB33 motif)

All 192 peaks (B-Box motif)

HeLa-S3, HMS (optimal IDR thresholded) 192 peaks (A-Box motif), after masking the B-Box motif BRF1 All 217 peaks (B-Box motif)

K562, HMS (optimal IDR thresholded) 220 peaks (A-Box motif), after masking the B-Box motif

All 316 peaks (AP1 motif), after using masking

HeLa-S3, Yale (SPP obtained from Factorbook)

BRG1 All 1544 peaks (GATA motif)

K562, Stanford (SPP obtained from Factorbook)

All 708 peaks (SP motif) HepG2, HAIB CBX1 (conservative IDR thresholded)

All 19951 peaks (SP motif)

K562, HMS CCNT2 (optimal IDR thresholded)

All 5774 peaks (IRF motif)

GM12878, HAIB CEBPB Protocol: v042211.1 (optimal IDR thresholded) 5759 peaks (RUNX motif), after masking the IRF motif

All 11382 peaks (SP motif)

HepG2, HAIB CEBPD Protocol: v041610.1 (optimal IDR thresholded)

Top 2000 peaks (SP motif) GM12878, Stanford (optimal IDR thresholded)

All 2184 peaks (SP motif)

H1-hESC, Stanford CHD1 (optimal IDR thresholded)

All 7226 peaks (SP motif)

H1-hESC, Broad (optimal IDR thresholded)

All 35861 peaks (SP motif)

HeLa-S3, Stanford (raw peaks)

All 28621 peaks (SP motif)

HepG2, Stanford CHD2 (raw peaks)

All 29104 peaks (SP motif) K562, Stanford (raw peaks)

All 3773 peaks (YY motif)

K562, Stanford DDX20 Target: eGFP-DDX20 (optimal IDR thresholded)

All 2227 peaks (SP motif)

GM12878, Yale (optimal IDR thresholded) 2184 peaks (NFY motif), after masking the SP motif

All 7628 peaks (a mix of primary AP1 motif and NFY motif)

K562, Yale FOS (optimal IDR thresholded)

All 5781 peaks (SP motif) K562, Yale (SPP obtained from Factorbook) 5601 peaks (a mix of primary AP1 motif and NFY motif)

All 4542 peaks (SP motif)

H1-hESC, Stanford (optimal IDR thresholded)

All 5414 peaks (SP motif)

HeLa-S3, Yale (SPP obtained from Factorbook)

All 5134 peaks (SP motif)

HUVEC, UTA (optimal IDR thresholded)

All 24096 peaks (SP motif) K562, Stanford (optimal IDR thresholded)

All 22384 peaks (SP motif)

K562, Stanford Treatment: IFNg for 30 minutes (SPP obtained from Factorbook)

All 5011 peaks (SP motif)

K562, Yale (optimal IDR thresholded)

All 7742 peaks (SP motif)

K562, Yale Treatment: IFNa for 30 minutes (optimal IDR thresholded)

All 10570 peaks (SP motif)

K562, Yale MYC Treatment: IFNa for 6 hours (optimal IDR thresholded)

All 19252 peaks (SP motif) K562, Yale Treatment: IFNg for 6 hours (optimal IDR thresholded)

All 11688 peaks (SP motif)

K562, UTA (optimal IDR thresholded)

All 4403 peaks (SP motif)

HepG2, UTA (optimal IDR thresholded)

All 25644 peaks (AP1 motif)

MCF10A-Er-Src, HMS Treatment: 1µM afimoxifene for 4 hours 25486 peaks (TEAD motif), after masking the AP1 motif (optimal IDR thresholded)

Top 25000 peaks (AP1 motif) MCF10A-Er-Src, HMS Treatment: 0.01% ethanol for 36 hours (optimal IDR thresholded)

All 26215 peaks (SP motif)

NB4, Stanford (optimal IDR thresholded)

All 15886 peaks (SP motif)

A549, HAIB Protocol: v041610.2 Treatment: 100nM dexamethasone for 1 hour (optimal IDR thresholded)

All 2902 peaks (SP motif)

ECC-1, HAIB, Replicate 1 Protocol: v042211.1 (raw peaks)

All 10018 peaks (SP motif)

ECC-1, HAIB, Replicate 2 Protocol: v042211.1 (raw peaks)

CREB1 All 6816 peaks (SP motif) K562, HAIB, Replicate 1 Protocol: v042211.1 (raw peaks)

All 9966 peaks (SP motif)

HepG2, HAIB, Replicate 1 Protocol: v042211.1 (raw peaks)

All 5299 peaks (SP motif)

HepG2, HAIB, Replicate 2 Protocol: v042211.1 (raw peaks)

All 23689 peaks (IRF motif)

GM12878, HAIB CREM (optimal IDR thresholded) Top 10000 peaks (SP motif)

All 5041 peaks (SP motif) HeLa-S3, USC (optimal IDR thresholded)

E2F1 All 10247 peaks (SP motif)

HeLa-S3, USC Target: HA-E2F1 (optimal IDR thresholded)

All 3429 peaks (SP motif)

GM12878, Stanford (optimal IDR thresholded)

All 2824 peaks (SP motif)

HeLa-S3, USC E2F4 (optimal IDR thresholded)

All 8170 peaks (SP motif)

K562, USC (optimal IDR thresholded)

All 3426 peaks (SP motif) HeLa-S3, USC (SPP obtained from Factorbook)

All 14305 peaks (SP motif)

K562, HAIB, Replicate 1 Protocol: v041610.2 (raw peaks)

E2F6 All 41821 peaks (SP motif)

K562, HAIB, Replicate 2 Protocol: v041610.2 (raw peaks)

All 11853 peaks (SP motif)

K562, USC (raw peaks)

All 22962 peaks (SP motif)

GM12878, HAIB Protocol: v041610.1 (optimal IDR thresholded)

All 10176 peaks (SP motif) MCF7, HAIB, Replicate 2 ELF1 Protocol: v042211.1 (raw peaks)

All 3558 peaks (SP motif)

SK-N-SH, HAIB, Replicate 2 Protocol: v042211.1 (raw peaks)

All 5577 peaks (SP motif)

GM12878, Stanford (optimal IDR thresholded)

ELK1 All 4807 peaks (SP motif)

HeLa-S3, Stanford (optimal IDR thresholded)

All 5514 peaks (SP motif)

A549, HAIB Protocol: v042211.1 Treatment: 0.02% ethanol for 1 hour Top 5000 peaks (ZNF143 motif) (optimal IDR thresholded) (optimal IDR thresholded)

All 4107 peaks (SP motif)

ETS1

GM12878, HAIB Protocol: PCR1x (optimal IDR thresholded) Top 500 peaks (ZBTB33 motif)

Top 2500 peaks (ZNF143 motif)

K562, HAIB Protocol: v041610.1 (optimal IDR thresholded)

All 10802 peaks (IRF motif)

GM12878, HAIB ETV6 (conservative IDR thresholded)

All 6484 peaks (SP motif) Astrocyte, Broad (optimal IDR thresholded)

All 5730 peaks (SP motif)

Fibroblast of dermis, Broad (optimal IDR thresholded)

All 2467 peaks (IRF motif)

GM12878, Broad EZH2 (optimal IDR thresholded)

All 1685 peaks (IRF motif)

K562, Broad (optimal IDR thresholded)

All 1721 peaks (SP motif)

T-cell acute lymphoblastic leukemia, Broad (optimal IDR thresholded)

All 1394 peaks (SP motif) H1-hESC, HAIB, Replicate 1 FOSL1 Protocol: v041610.2 (raw peaks)

All 22846 peaks (IRF motif)

GM12878, HAIB FOXM1 Protocol: v042211.1 (optimal IDR thresholded) Top 500 peaks (IRF motif)

All 18140 peaks (SP motif)

PFSK-1, HAIB Protocol: PCR2x (optimal IDR thresholded) Top 500 peaks (SP motif)

FOXP2

All 14659 peaks (IRF motif) SK-N-MC, HAIB Protocol: PCR2x (optimal IDR thresholded)

All 12314 peaks (SP motif)

A549, HAIB Protocol: v042211.1 Treatment: 0.02% ethanol for 1 hour (optimal IDR thresholded)

All 14322 peaks (SP motif)

K562, HAIB Protocol: v041610.1 (optimal IDR thresholded)

Top 8000 peaks (SP motif)

HepG2, HAIB Protocol: PCR2x (optimal IDR thresholded)

GABPA All 9548 peaks (SP motif)

MCF7, HAIB, Replicate 1 Protocol: v042211.1 (raw peaks)

All 4319 peaks (SP motif) SK-N-SH, HAIB, Replicate 1 Protocol: v042211.1 (raw peaks)

All 6682 peaks (SP motif)

SK-N-SH, HAIB, Replicate 2 Protocol: v042211.1 (raw peaks)

All 24222 peaks (TEAD motif)

HUVEC, USC GATA2 (SPP obtained from Factorbook) 24178 peaks (AP1 motif), after masking the TEAD motif

Top 5000 peaks (FOXA motif)

T47D, USC Protocol: v041610.2 GATA3 Treatment: 0.02% dimethyl sulfoxide for 1 hour Top 15000 peaks (FOXA motif) (optimal IDR thresholded) (optimal IDR thresholded)

All 2918 peaks (SP motif)

K562, HMS GTF2B (optimal IDR thresholded)

All 11780 peaks (SP motif)

K562, Stanford HDAC1 (optimal IDR thresholded)

Top 5000 peaks (FOXA motif)

HepG2, HA HDAC2 Protocol: v041610.1 (optimal IDR thresholded)

All 14436 peaks (SP motif)

K562, HMS HMGN3 (optimal IDR thresholded)

Top 500 peaks (B-Box motif) HepG2, Stanford HSF1 Treatment: forskolin for 6 hours (optimal IDR thresholded)

Top 500 peaks (YY motif)

K562, Stanford ID3 Target: eGFP-ID3 (conservative IDR thresholded) Top 2500 peaks (YY motif)

All 9045 peaks (IRF motif)

GM12878, USC IKZF1 (optimal IDR thresholded) Top 500 peaks (IRF motif)

All 1601 peaks (YY motif) K562, Stanford ILK Target: eGFP-ILK (optimal IDR thresholded)

All 12499 peaks (SP motif)

K562, Stanford IRF1 Treatment: IFNg for 6 hours (optimal IDR thresholded)

All 1575 peaks (SP motif)

HeLa-S3, Stanford (optimal IDR thresholded) 1569 peaks (NFY motif), after masking the SP motif

IRF3

All 684 peaks (NFY motif)

HepG2, Stanford (optimal IDR thresholded)

All 17404 peaks (RUNX motif) GM12878, HAIB IRF4 Protocol: PCR1x (optimal IDR thresholded)

Top 500 peaks (YY motif)

K562, Stanford IRF9 (optimal IDR thresholded) Top 3000 peaks (YY motif)

All 24252 peaks (SP motif)

A549, HAIB, Replicate 2 Protocol: v041610.2 Treatment: 0.02% ethanol for 1 hour (raw peaks)

All 8418 peaks (SP motif)

H1-hESC, HAIB JUND Protocol: v041610.2 (optimal IDR thresholded)

All 759 peaks (SP motif) K562, Yale (SPP obtained from Factorbook)

All 1170 peaks (SP motif)

HeLa-S3, Stanford KAT2A (raw peaks)

Top 500 peaks (YY motif)

H1-hESC, Broad KDM5A (optimal IDR thresholded) 1612 peaks (NFKB motif), after masking noise

All 15442 peaks (SP motif)

K562, Broad KDM5B (optimal IDR thresholded)

All 8583 peaks (SP motif) K562, Stanford KLF1 (optimal IDR thresholded)

All 9853 peaks (SP motif)

A549, Stanford (optimal IDR thresholded)

All 12533 peaks (SP motif)

GM12878, Stanford (optimal IDR thresholded)

All 11809 peaks (SP motif)

HepG2, Stanford (optimal IDR thresholded)

All 31357 peaks (SP motif)

K562, Stanford MAX (optimal IDR thresholded)

All 12393 peaks (SP motif) MCF-7, HAIB, Replicate 2 Protocol: v042211.1 (raw peaks)

All 34553 peaks (ETS motif)

NB4, Stanford (optimal IDR thresholded) Top 25000 peaks (SP motif)

Top 500 peaks (FOXA motif)

HepG2, HAIB MBD4 Protocol: v042211.1 (optimal IDR thresholded) Top 1000 peaks (FOXA motif)

All 17536 peaks (IRF motif) GM12878, HAIB MEF2A Protocol: PCR1x (optimal IDR thresholded) 17184 peaks (RUNX motif), after masking the IRF motif

All 9815 peaks (IRF motif)

GM12878, HAIB MEF2C Protocol: v041610.1 (optimal IDR thresholded) 9035 peaks (RUNX motif), after masking the IRF motif

All 12009 peaks (IRF motif)

GM12878, HAIB MTA3 Protocol: v042211.1 (optimal IDR thresholded)

All 17709 peaks (SP motif) GM12878, Stanford (optimal IDR thresholded)

All 6345 peaks (SP motif)

H1-hESC, Stanford (optimal IDR thresholded)

All 11979 peaks (SP motif)

HeLa-S3, Stanford MXI1 (optimal IDR thresholded)

All 20325 peaks (SP motif)

HepG2, Stanford (optimal IDR thresholded)

All 6695 peaks (SP motif)

K562, Stanford (optimal IDR thresholded)

All 5462 peaks (SOX2 motif) H1-hESC, HAIB NANOG Protocol: v041610.2 (optimal IDR thresholded) Top 2500 peaks (SOX2 motif)

All 10855 peaks (IRF motif)

GM12878, Stanford (raw peaks) 6492 peaks (USF motif), after masking the IRF motif

NFE2 All 761 peaks (USF motif)

GM12878, Stanford (optimal IDR thresholded) 766 peaks (SP motif), after masking the USF motif All 9254 peaks (IRF motif)

GM10847, Stanford Treatment: 25ng/mL TNFa for 6 hours (optimal IDR thresholded)

All 16962 peaks (IRF motif)

GM12878, Stanford Treatment: 25ng/mL TNFa for 6 hours (optimal IDR thresholded)

All 28652 peaks (IRF motif)

GM12891, Stanford Treatment: 25ng/mL TNFa for 6 hours (optimal IDR thresholded)

RELA/NFKB All 12795 peaks (SP motif)

GM15510, Stanford Treatment: 25ng/mL TNFa for 6 hours (optimal IDR thresholded)

All 8800 peaks (IRF motif) GM18505, Stanford Treatment: 25ng/mL TNFa for 6 hours (optimal IDR thresholded)

All 13515 peaks (IRF motif)

GM18951, Stanford Treatment: 25ng/mL TNFa for 6 hours (optimal IDR thresholded)

All 5950 peaks (SP motif)

HeLa-S3, HMS NFYA (optimal IDR thresholded)

All 17471 peaks (SP motif)

HepG2, HAIB, Replicate 2 NRSF/REST Protocol: v041610.1 (raw peaks)

Top 2000 peaks (FOXA motif)

HepG2, HAIB NFIC Protocol: v042211.1 (optimal IDR thresholded) Top 9000 peaks (FOXA motif) Top 6000 peaks (GATA1-TAL1 motif)

K562, HAIB NR2F2 Protocol: v042211.1 (optimal IDR thresholded) Top 7000 peaks (GATA1-TAL1 motif)

All 5154 peaks (IRF motif)

GM12878, HAIB Protocol: PCR1x (optimal IDR thresholded) 5062 peaks (RUNX motif), after masking the IRF motif

All 17442 peaks (IRF motif) GM12878, Stanford (optimal IDR thresholded) 17400 peaks (RUNX motif), after masking the IRF motif

All 6186 peaks (IRF motif)

GM12878, Stanford, 2 (optimal IDR thresholded) 6154 peaks (RUNX motif), after masking the IRF motif

All 2722 peaks (SP motif)

H1-hESC, HAIB, Replicate 1 Protocol: v041610.2 (raw peaks)

All 11069 peaks (SP motif) H1-hESC, HAIB, Replicate 2 P300/EP300 Protocol: v041610.2 (raw peaks)

All 8890 peaks (SP motif)

H1-hESC, HAIB Protocol: v041610.2 (optimal IDR thresholded)

All 25804 peaks (AP1 motif)

HeLa-S3, Stanford (optimal IDR thresholded) Top 3000 peaks (CEBPB motif)

All 22375 peaks (FOXA motif)

HepG2, HAIB Protocol: v041610.1 (SPP obtained from Factorbook)

Top 10000 peaks (GATA1-TAL1 motif) K562, Stanford (optimal IDR thresholded)

Top 8000 peaks (FOXA motif)

T47D, HAIB Protocol: v041610.2 Treatment: 0.02% dimethyl sulfoxide for 1 hour Top 8500 peaks (FOXA motif) (optimal IDR thresholded)

All 25197 peaks (SP motif)

GM12878, HA Target: PAX5-C20, Protocol: PCR1x (optimal IDR thresholded)

PAX5 All 10088 peaks (SP motif)

GM12892, HA Protocol: v041610.1 (optimal IDR thresholded)

All 5628 peaks (SP motif) A549, HAIB, Replicate 1 Protocol: v042211.1 (optimal IDR thresholded)

PBX3 All 6052 peaks (SP motif)

A549, HAIB, Replicate 2 Protocol: v042211.1 (optimal IDR thresholded)

All 429 peaks (HSF motif)

HepG2, Stanford PGC1A Treatment: forskolin (SPP obtained from Factorbook)

All 22082 peaks (SP motif)

K562, Broad PHF8 (optimal IDR thresholded)

All 16642 peaks (SP motif)

GM12878, HAIB Protocol: v042211.1 (optimal IDR thresholded)

Top 3500 peaks (GATA1-TAL1 motif) K562, HAIB PML Protocol: v042211.1 (optimal IDR thresholded)

All 4788 peaks (SP motif)

MCF-7, HAIB, Replicate 1 Protocol: v042211.1 (optimal IDR thresholded)

All 20591 peaks (SP motif)

ECC-1, HAIB, Replicate 1 Protocol: v041610.2 Treatment: 0.02% dimethyl sulfoxide for 1 hour (raw peaks)

All 35893 peaks (SP motif)

ECC-1, HAIB, Replicate 2 Protocol: v041610.2 POLR2A Treatment: 0.02% dimethyl sulfoxide for 1 hour (raw peaks)

All 4073 peaks (SP motif)

HepG2, Stanford Target: POLR2AphosphoS2 (optimal IDR thresholded)

2282 peaks (A-Box motif), , after using masking HeLa-S3, HMS (SPP obtained from Factorbook)

1285 peaks (B-Box motif), after using masking

K562, HMS (optimal IDR thresholded)

POLR3A /RPC155 All 903 peaks (B-Box motif)

K562, HMS (SPP obtained from Factorbook) 913 peaks (A-Box motif), after masking the B-Box motif

All 210 peaks (B-Box motif)

GM12878, Yale (optimal IDR thresholded) 210 peaks (A-Box motif), after masking the B-Box motif POLR3G /RPC32 All 207 peaks (B-Box motif)

K562, Stanford (optimal IDR thresholded) 206 peaks (A-Box motif), after masking the B-Box motif

All 22777 peaks (IRF motif)

GM12878, HAIB Protocol: PCR1x (optimal IDR thresholded)

POU2F2 All 14583 peaks (SP motif)

GM12891, HAIB Protocol: PCR1x (optimal IDR thresholded)

All 3793 peaks (YY motif) K562, HAIB PTRF Target: eGFP-PTRF (optimal IDR thresholded)

Top 1000 peaks (YY motif)

K562, Stanford PYGO2 (optimal IDR thresholded) All 4577 peaks (YY motif)

All 35572 peaks (CTCF motif)

GM12878, HAIB Protocol: v041610.1 (SPP obtained from Factorbook)

All 27134 peaks (CTCF motif)

GM12878, Stanford (SPP obtained from Factorbook)

RAD21 All 48575 peaks (CTCF motif) H1-hESC, Stanford (SPP obtained from Factorbook)

All 35240 peaks (CTCF motif)

HeLa-S3, Stanford (SPP obtained from Factorbook)

All 14116 peaks (SP motif)

K562, Broad RBBP5 (optimal IDR thresholded)

All 5315 peaks (SP motif)

HepG2, Stanford (optimal IDR thresholded)

Top 500 peaks (GATA1-TAL1 motif)

K562, Stanford (optimal IDR thresholded) Top 700 peaks (GATA1-TAL1 motif) RCOR1 Top 2000 peaks (GATA1-TAL1 motif)

Top 5000 peaks (GATA1-TAL1 motif)

K562, Stanford, 2 (optimal IDR thresholded)

Top 6000 peaks (GATA1-TAL1 motif)

All 67670 peaks (IRF motif)

GM12878, HAIB RUNX3 Protocol: v042211.1 (optimal IDR thresholded)

All 4328 peaks (SP motif) GM12878, Stanford (optimal IDR thresholded)

All 5994 peaks (SP motif)

HepG2, Stanford RFX5 (optimal IDR thresholded)

All 2194 peaks (SP motif)

K562, Stanford (optimal IDR thresholded)

All 9720 peaks (SP motif)

K562, Broad SAP30 (optimal IDR thresholded)

All 6004 peaks (SP motif)

A549, HAIB Treatment: 0.02% ethanol for 1 hour (optimal IDR thresholded)

All 10342 peaks (SP motif) GM12878, Stanford (optimal IDR thresholded)

All 8943 peaks (SP motif)

Top 1000 peaks (NRSF motif)

H1-hESC, HAIB Protocol: PCR1x (optimal IDR thresholded)

Top 3000 peaks (NRSF motif)

All 21250 peaks (SP motif)

SIN3A Top 500 peaks (NRSF motif) H1-hESC, Stanford (optimal IDR thresholded) Top 1000 peaks (NRSF motif)

Top 2000 peaks (NRSF motif)

All 10391 peaks (SP motif)

HepG2, HAIB Protocol: PCR1x (SPP obtained from Factorbook)

All 8063 peaks (SP motif)

K562, HAIB Protocol: v041610.1 (SPP obtained from Factorbook)

All 7100 peaks (SP motif) PANC1, HAIB Protocol: v041610.1 (optimal IDR thresholded)

All 2301 peaks (GATA motif)

K562, HMS SIRT6 (optimal IDR thresholded)

All 4788 peaks (ZNF143 motif)

GM12878, HAIB Protocol: PCR1x (optimal IDR thresholded)

All 3328 peaks (ZNF143 motif)

H1-hESC, HAIB Protocol: PCR1x (optimal IDR thresholded)

SIX5 All 4155 peaks (ZNF143 motif)

K562, HAIB Protocol: PCR1x (optimal IDR thresholded)

All 4148 peaks (ZNF143 motif) K562, HAIB, Replicate 2 Protocol: v041610.1 (raw peaks)

All 7953 peaks (SP motif)

GM12878, HAIB (optimal IDR thresholded)

SMAD5 All 12533 peaks (SP motif)

K562, HAIB (conservative IDR thresholded)

All 7772 peaks (SP motif)

SMARCB1/ K562, Stanford INI1 (optimal IDR thresholded)

All 30402 peaks (CTCF motif)

GM12878, Stanford (optimal IDR thresholded)

All 39472 peaks (CTCF motif) HeLa-S3, Stanford (optimal IDR thresholded)

SMC3 All 30687 peaks (CTCF motif)

HepG2, Stanford (optimal IDR thresholded)

All 23577 peaks (CTCF motif)

K562, Stanford (optimal IDR thresholded)

Top 14500 peaks (HNF4 motif)

HepG2, HAIB SP1 Protocol: PCR1x (SPP obtained from Factorbook)

All 2621 peaks (NRSF motif)

HepG2, HAIB SP2 Protocol: v042211.1 (optimal IDR thresholded)

All 2583 peaks (SP motif) HepG2, Stanford SREBF1 Treatment: insulin for 6 hours (optimal IDR thresholded)

All 103 peaks (SP motif)

HepG2, Yale Treatment: 2µM pravastatin for 16 SREBF2 hours (raw peaks)

All 3841 peaks (SP motif)

ECC-1, HAIB, Replicate 2 Protocol: v042211.1 (raw peaks)

All 8478 peaks (SP motif)

GM12878, HAIB Protocol: PCR2x (optimal IDR thresholded)

All 2404 peaks (ETS motif)

GM12878, HAIB Protocol: PCR2x (SPP obtained from Factorbook)

All 9071 peaks (ETS motif) GM12878, HAIB SRF Protocol: v041610.1 (SPP obtained from Factorbook)

All 2309 peaks (AP1 motif), after masking noise

HCT116, HAIB, Replicate 1 Protocol: v042211.1 (raw peaks)

All 4700 peaks (SP motif)

K562, HAIB Protocol: v041610.1 (optimal IDR thresholded)

All 6148 peaks (SP motif)

MCF-7, HAIB, Replicate 2 Protocol: v042211.1 (raw peaks)

All 1769 peaks (SP motif)

GM12878, Stanford (optimal IDR thresholded)

All 1502 peaks (IRF motif) K562, Yale STAT1 Treatment: IFNa for 30 minutes (optimal IDR thresholded)

All 1474 peaks (IRF motif)

K562, Yale Treatment: IFNa for 6 hours (optimal IDR thresholded)

Top 1000 peaks (IRF motif)

K562, Yale Treatment: IFNa for 30 minutes (SPP obtained from Factorbook)

STAT2 All 1922 peaks (IRF motif)

K562, Yale Treatment: IFNa for 6 hours (optimal IDR thresholded)

All 6483 peaks (IRF motif)

GM12878, Stanford (optimal IDR thresholded)

All 10109 peaks (AP1 motif) HeLa-S3, Stanford (SPP obtained from Factorbook) 10082 peaks (TEAD motif), after masking the AP1 motif

All 44934 peaks (AP1 motif)

MCF10A-Er-Src, HMS Treatment: 0.01% ethanol for 4 hours (optimal IDR thresholded)

All 41169 peaks (AP1 motif)

MCF10A-Er-Src, HMS Treatment: 0.01% ethanol for 12 STAT3 hours 40971 peaks (TEAD motif), after masking the AP1 motif (optimal IDR thresholded)

All 39680 peaks (AP1 motif) MCF10A-Er-Src, HMS Treatment: 1µM afimoxifene for 12 hours 39282 peaks (TEAD motif), after masking the AP1 motif (optimal IDR thresholded)

All 44330 peaks (AP1 motif)

MCF10A-Er-Src, HMS Treatment: 1µM afimoxifene for 36 hours 44047 peaks (TEAD motif), after masking the AP1 motif (optimal IDR thresholded)

All 7401 peaks (IRF motif)

GM12878, HAIB Protocol: v042211.1 (optimal IDR thresholded)

STAT5A Top 6500 peaks (GATA1-TAL1 motif) K562, HAIB Protocol: v042211.1 (optimal IDR thresholded)

All 3302 peaks (SP motif)

NT2-D1, USC SUZ12 (optimal IDR thresholded)

All 9936 peaks (SP motif)

A549, HAIB Protocol: v042211.1 Treatment: 0.02% ethanol for 1 hour (optimal IDR thresholded)

All 14235 peaks (SP motif)

GM12878, HAIB Protocol: PCR1x (optimal IDR thresholded)

All 20516 peaks (SP motif)

H1-hESC, HAIB Protocol: v041610.2 (optimal IDR thresholded)

All 16057 peaks (SP motif) HeLa-S3, HAIB Protocol: PCR1x (optimal IDR thresholded)

TAF1 All 15134 peaks (SP motif)

HepG2, HAIB Protocol: PCR2x (SPP obtained from Factorbook)

All 15684 peaks (SP motif)

K562, HAIB Protocol: v041610.1 (SPP obtained from Factorbook)

All 5826 peaks (SP motif)

PFSK-1, HAIB Protocol: v041610.1 (optimal IDR thresholded)

All 13937 peaks (SP motif)

SK-N-SH, HAIB Protocol: v041610.1 (optimal IDR thresholded)

All 4552 peaks (SP motif) H1-hESC, HAIB, Replicate 1 Protocol: v041610.2 (raw peaks)

All 3413 peaks (SP motif)

K562, HAIB TAF7 Protocol: v041610.1 (optimal IDR thresholded)

Top 1500 peaks (YY motif)

K562, Stanford Target: eGFP-TAF7 (optimal IDR thresholded)

All 13672 peaks (IRF motif)

GM12878, Stanford (optimal IDR thresholded) Top 500 peaks (IRF motif)

TBL1XR1

Top 1500 peaks (GATA1-TAL1 motif) K562, Stanford (optimal IDR thresholded)

Top 200 peaks (B-Box motif)

GM12878, Stanford (optimal IDR thresholded)

All 17146 peaks (SP motif)

H1-hESC, Stanford (optimal IDR thresholded) Top 200 peaks (B-Box motif)

Top 200 peaks (B-Box motif)

HeLa-S3, Stanford (optimal IDR thresholded)

TBP All 13753 peaks (SP motif) HepG2, Stanford (optimal IDR thresholded) Top 200 peaks (B-Box motif)

All 17513 peaks (SP motif)

K562, Stanford (optimal IDR thresholded) Top 200 peaks (B-Box motif)

All 2058 peaks (FOXA motif)

HepG2, HAIB Protocol: PCR1x (optimal IDR thresholded)

TCF12 Top 200 peaks (B-Box motif) MCF7, HAIB, Replicate 1 Protocol: v042211.1 (raw peaks)

All 7208 peaks (IRF motif)

GM12878, HAIB (optimal IDR thresholded)

TCF7 All 3491 peaks (SP motif)

K562, HAIB (optimal IDR thresholded)

Top 10000 peaks (SP motif)

HCT116, USC TCF7L2 (optimal IDR thresholded)

Top 6000 peaks (NRSF motif)

A549, HAIB, Replicate 1 Protocol: v042211.1 (raw peaks)

5659 peaks (AP1 motif), after masking noise A549, HAIB, Replicate 2 Protocol: v042211.1 (raw peaks)

2630 peaks (AP1 motif), after masking noise

HCT116, HAIB, Replicate 1 Protocol: v042211.1 (raw peaks)

2193 peaks (AP1 motif), after masking noise

HCT116, HAIB, Replicate 2 Protocol: v042211.1 (raw peaks)

Top 8500 peaks (FOXA motif)

TEAD4

HepG2, HAIB Protocol: v042211.1 (optimal IDR thresholded) Top 9000 peaks (FOXA motif)

Top 17000 peaks (GATA1-TAL1 motif) K562, HAIB Protocol: v042211.1 (optimal IDR thresholded) Top 18500 peaks (GATA1-TAL1 motif)

11186 peaks (AP1 motif), after masking noise

SK-N-SH, HAIB, Replicate 1 Protocol: v042211.1 (raw peaks)

All 3476 peaks (SP motif)

K562, HAIB THAP1 Protocol: v041610.1 (optimal IDR thresholded)

Top 200 peaks (SP motif)

GM12878, USC (optimal IDR thresholded)

All 2112 peaks (SP motif) HeLa-S3, USC (optimal IDR thresholded) Top 1500 peaks (ETS motif)

TR4/NR2C2 All 2943 peaks (SP motif)

HepG2, USC (optimal IDR thresholded) Top 500 peaks (ETS motif)

All 581 peaks (SP motif)

K562, USC (optimal IDR thresholded)

All 19859 peaks (SP motif) A549, HAIB, Replicate 1 Treatment: 0.02% ethanol for 1 hour (raw peaks)

All 8763 peaks (SP motif)

HepG2, HAIB, Replicate 2 YY1 Protocol: v041610.1 (raw peaks)

All 23975 peaks (SP motif)

K562, HAIB Protocol: v041610.2 (optimal IDR thresholded)

All 5824 peaks (IRF motif)

GM12878, HAIB (conservative IDR thresholded)

ZBED1 All 2970 peaks (SP motif)

K562, HAIB (conservative IDR thresholded)

Top 1500 peaks (SP motif) A549, HAIB Protocol: v042211.1 Treatment: 0.02% ethanol for 1 hour (optimal IDR thresholded)

All 2139 peaks (SP motif)

GM12878, HAIB Protocol: PCR1x (optimal IDR thresholded)

All 4307 peaks (SP motif)

HCT116, HAIB Protocol: v041610.1 (optimal IDR thresholded)

ZBTB33 All 2869 peaks (SP motif)

HepG2, HAIB Protocol: PCR1x (optimal IDR thresholded)

All 1686 peaks (SP motif)

HepG2, HAIB Protocol: v041610.1 (SPP obtained from Factorbook)

All 3274 peaks (SP motif) K562, HAIB Protocol: PCR1x (optimal IDR thresholded)

Top 500 peaks (SP motif)

K562, HAIB ZBTB7A Protocol: v041610.1 (optimal IDR thresholded)

All 7536 peaks (SP motif)

HepG2, HAIB ZHX2 (optimal IDR thresholded)

All 19902 peaks (CTCF motif)

GM12878, Stanford (optimal IDR thresholded)

All 30588 peaks (CTCF motif)

H1-hESC, Stanford ZNF143 (optimal IDR thresholded)

All 29030 peaks (CTCF motif) K562, Stanford (optimal IDR thresholded)