Predicting active enhancers with DNA methylation and histone modification

BMC Bioinformatics

Table 2 Comparison with two recently published methods, iEnhancer-RD and LSTMAtt

Cell	Method	Sn	Sp	AUC	MCC	F1-score
GM12878	iEnhancer-RD	0.1323	0.9471	0.6494	0.1135	0.1774
	LSTMAtt	0.2838	0.8068	0.2290	0.0783	0.2325
	eRNA_RF_methyl_H3K27ac	0.9315	0.9433	0.9374	0.7942	0.8203
	eRNA_RF_methyl_H3K27ac_gene	0.9780	0.9445	0.9613	0.8277	0.8467
	eRNA_XGBoost_methyl_H3K27ac	0.9634	0.9317	0.9475	0.7890	0.8122
	eRNA_XGBoost_methyl_H3K27ac_gene	0.9780	0.9397	0.9589	0.8166	0.8363
K562	iEnhancer-RD	0.1361	0.9855	0.7181	0.1690	0.1800
	LSTMAtt	0.3849	0.8132	0.3131	0.0956	0.1257
	eRNA_RF_methyl_H3K27ac	0.9719	0.9541	0.9630	0.6491	0.6207
	eRNA_RF_methyl_H3K27ac_gene	0.9883	0.9575	0.9729	0.6721	0.6444
	eRNA_XGBoost_methyl_H3K27ac	0.9386	0.9536	0.9461	0.6271	0.6020
	eRNA_XGBoost_methyl_H3K27ac_gene	0.9442	0.9573	0.9508	0.6465	0.6239
HepG2	iEnhancer-RD	0.1752	0.9709	0.7260	0.2001	0.2276
	LSTMAtt	0.3667	0.8213	0.3012	0.1268	0.2087
	eRNA_RF_methyl_H3K27ac	0.9612	0.9515	0.9564	0.7520	0.7559
	eRNA_RF_methyl_H3K27ac_gene	0.9849	0.9476	0.9663	0.7535	0.7534
	eRNA_XGBoost_methyl_H3K27ac	0.9410	0.9453	0.9431	0.7191	0.7242
	eRNA_XGBoost_methyl_H3K27ac_gene	0.9812	0.9429	0.9620	0.7360	0.7351

ISSN: 1471-2105