ENNGene: an Easy Neural Network model building tool for Genomics

Chalupová, Eliška; Vaculík, Ondřej; Poláček, Jakub; Jozefov, Filip; Majtner, Tomáš; Alexiou, Panagiotis

doi:10.1186/s12864-022-08414-x

BMC Genomics

Table 1 AUROC values from the evaluation of the final models, together with the RBP24 dataset properties. Models created using ENNGene outperform the state-of-the-art tools on more than half of the experiments in the RBP24 dataset while also improving the average AUROC value on the whole dataset. The AUROC values of the other tools are

From: ENNGene: an Easy Neural Network model building tool for Genomics

Protein	RBP-24
	Dataset info			Results (AUROC)
	Clip method	# positives	# negatives	GraphProt	deepnet-rbp	DeepBind	iDeepV	iDeepE	DeepRKE	ENNGene
Ago1-4	PAR-CLIP	36,902	31,310	0.895	0.881	0.919	0.925	0.915	0.932	0.927
Ago2	HITS-CLIP	48,095	44,251	0.765	0.809	0.879	0.886	0.884	0.9	0.94
ALKBH5	PAR-CLIP	1213	1197	0.68	0.714	0.668	0.643	0.758	0.74	0.877
C17ORF85	PAR-CLIP	1860	1849	0.8	0.82	0.755	0.74	0.83	0.824	0.916
C22ORF28	PAR-CLIP	9369	9136	0.751	0.792	0.809	0.823	0.837	0.832	0.908
CAPRIN1	PAR-CLIP	8140	7901	0.855	0.834	0.888	0.824	0.893	0.869	0.896
ELAVL1	HITS-CLIP	8595	8436	0.955	0.966	0.98	0.966	0.964	0.978	0.991
	PAR-CLIP (A)	27,275	23,974	0.959	0.966	0.972	0.973	0.988	0.978	0.965
	PAR-CLIP (B)	9464	9283	0.935	0.961	0.961	0.962	0.971	0.98	0.987
	PAR-CLIP (C)	125,202	113,686	0.991	0.994	0.989	0.99	0.979	0.996	0.989
EWSR1	PAR-CLIP	16,292	14,720	0.935	0.966	0.969	0.962	0.969	0.971	0.972
FUS	PAR-CLIP	34,581	31,480	0.968	0.98	0.983	0.976	0.985	0.988	0.977
hnRNPC	iCLIP	21,472	19,794	0.952	0.962	0.979	0.979	0.976	0.978	0.977
IGF2BP1-3	PAR-CLIP	8539	6838	0.889	0.879	0.939	0.923	0.947	0.943	0.946
MOV10	PAR-CLIP	13,793	12,987	0.863	0.854	0.899	0.896	0.916	0.92	0.922
PUM2	PAR-CLIP	9116	8227	0.954	0.971	0.964	0.965	0.967	0.965	0.972
PTB	HITS-CLIP	44,574	43,700	0.937	0.983	0.944	0.936	0.944	0.953	0.954
QKI	PAR-CLIP	10,276	9142	0.957	0.983	0.973	0.965	0.97	0.975	0.984
SFRS1	HITS-CLIP	19,438	17,195	0.898	0.931	0.929	0.905	0.946	0.945	0.939
TAF15	PAR-CLIP	7298	6606	0.97	0.983	0.978	0.978	0.976	0.985	0.985
TDP43	iCLIP	92,031	75,079	0.874	0.876	0.93	0.935	0.945	0.954	0.924
TIA1	iCLIP	18,049	16,135	0.861	0.891	0.929	0.941	0.937	0.942	0.959
TIAL1	iCLIP	42,332	36,652	0.833	0.87	0.922	0.929	0.934	0.946	0.95
ZC3H7B	PAR-CLIP	20,962	20,018	0.82	0.796	0.875	0.883	0.907	0.914	0.862
	AVERAGE AUROC:			0.887	0.903	0.918	0.913	0.931	0.934	0.947

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ISSN: 1471-2164

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