Table 2 The comparison of prediction performances with different input signals.

Cell line	TF/HM	CNN		SVM
Cell line	TF/HM	DNase I only	+TF/HM	+TF/HM
A549	RAD21	0.948 ± 0.001	0.964 ± 0.001	0.887 ± 0.001
H1-hESC		0.937 ± 0.001	0.963 ± 0.001	0.773 ± 0.001
HCT116		0.944 ± 0.003	0.956 ± 0.002	0.888 ± 0.001
MCF-7		0.945 ± 0.001	0.956 ± 0.001	0.898 ± 0.004
SK-N-SH_RA		0.907 ± 0.003	0.967 ± 0.002	0.886 ± 0.004
GM12878	RAD21	0.926 ± 0.002	0.970 ± 0.001	0.881 ± 0.004
	SMC3		0.957 ± 0.001	0.841 ± 0.003
	2 TFs		0.972 ± 0.001	0.889 ± 0.004
	2 TFs, H2AFZ		0.970 ± 0.002	0.890 ± 0.001
HeLa-S3	RAD21	0.941 ± 0.002	0.968 ± 0.002	0.855 ± 0.004
	SMC3		0.968 ± 0.002	0.854 ± 0.003
	2 TFs		0.968 ± 0.001	0.855 ± 0.002
	TFs, H2AFZ		0.967 ± 0.002	0.855 ± 0.003
HepG2	RAD21	0.847 ± 0.007	0.949 ± 0.001	0.874 ± 0.002
	SMC3		0.920 ± 0.002	0.852 ± 0.003
	2 TFs		0.950 ± 0.002	0.883 ± 0.002
	2 TFs, H3K4me1		0.949 ± 0.003	0.884 ± 0.002
K562	RAD21	0.951 ± 0.001	0.970 ± 0.001	0.888 ± 0.002
	SMC3		0.961 ± 0.001	0.870 ± 0.000
	2 TFs		0.973 ± 0.001	0.902 ± 0.000
	2 TFs, H2AFZ		0.972 ± 0.002	0.902 ± 0.004

The “ + TF/HM” column refers to the extra information added to the prediction model, and the “2 TFs” refers to RAD21 and SMC3. The AUPRC values are the average of three cross-validation folds with standard errors given in parentheses.

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