Self-organizing maps with variable neighborhoods facilitate learning of chromatin accessibility signal shapes associated with regulatory elements

Table 1 Generalization of shapes across cell type was cell type dependent

Training sample	Testing sample	Promoter		Enhancer		Weak
Training sample	Testing sample	Precision	Recall	Precision	Recall	Precision	Recall
A549	A549	0.39	0.84	0.31	0.06	0.88	0.76
	Brain (H)	0.16	0.79	0.38	0.05	0.89	0.62
	H1 (L)	0.19	0.91	0.28	0.10	0.90	0.26
Brain (H)	Brain (H)	0.45	0.26	0.33	0.34	0.75	0.80
	A549	0.72	0.25	0.24	0.30	0.66	0.83
	H1 (L)	0.74	0.13	0.26	0.33	0.80	0.86
H1 (L)	H1 (L)	0.37	0.72	N/A^a	N/A	0.81	0.90
	A549	0.47	0.69	N/A	N/A	0.66	0.77
	Brain (H)	0.20	0.62	N/A	N/A	0.74	0.75

^aN/A values indicate that no shapes were learned for the corresponding RE in the corresponding sample

ISSN: 1471-2105