Deep neural networks for inferring binding sites of RNA-binding proteins by using distributed representations of RNA primary sequence and secondary structure

Table 2 Performance comparison between DeepRKE, GraphProt, deepnet-rbp, DeepBind and iDeepV on RBP-24 dataset

RBP	#positives	#negatives	GraphProt	deepnet-rbp	DeepBind	iDeepV	DeepRKE
ALKBH5 PAR-CLIP	1213	1197	0.680	0.714	0.668	0.643	0.740
C17ORF85 PAR-CLIP	1860	1849	0.800	0.820	0.755	0.740	0.824
C22ORF28 PAR-CLIP	9369	9136	0.751	0.792	0.809	0.823	0.832
CAPRIN1 PAR-CLIP	8140	7901	0.855	0.834	0.888	0.824	0.869
Ago2 HITS-CLIP	48,095	44,251	0.765	0.809	0.879	0.886	0.900
ELAVL1 HITS-CLIP	8595	8436	0.955	0.966	0.980	0.966	0.978
SFRS1 HITS-CLIP	19,438	17,195	0.898	0.931	0.929	0.905	0.945
HNRNPC iCLIP	21,472	19,794	0.952	0.962	0.979	0.979	0.978
TDP43 iCLIP	92,031	75,079	0.874	0.876	0.930	0.935	0.954
TIA1 iCLIP	18,049	16,135	0.861	0.891	0.929	0.941	0.942
TIAL1 iCLIP	42,332	36,652	0.833	0.870	0.922	0.929	0.946
Ago1-4 PAR-CLIP	36,902	31,310	0.895	0.881	0.919	0.925	0.932
ELAVL1 PAR-CLIP(B)	9464	9283	0.935	0.961	0.961	0.962	0.980
ELAVL1 PAR-CLIP (A)	27,275	23,974	0.959	0.966	0.972	0.973	0.978
EWSR1 PAR-CLIP	16,292	14,720	0.935	0.966	0.969	0.962	0.971
FUS PAR-CLIP	34,581	31,480	0.968	0.980	0.983	0.976	0.988
ELAVL1 PAR-CLIP(C)	125,202	113,686	0.991	0.994	0.989	0.990	0.996
IGF2BP1-3 PAR-CLIP	8539	6838	0.889	0.879	0.939	0.923	0.943
MOV10 PAR-CLIP	13,793	12,987	0.863	0.854	0.899	0.896	0.920
PUM2 PAR-CLIP	9116	8227	0.954	0.971	0.964	0.965	0.965
QKI PAR-CLIP	10,276	9142	0.957	0.983	0.973	0.965	0.975
TAF15 PAR-CLIP	7298	6606	0.970	0.983	0.978	0.978	0.985
PTB HITS-CLIP	44,574	43,700	0.937	0.983	0.944	0.936	0.953
ZC3H7B PAR-CLIP	20,962	20,018	0.820	0.796	0.875	0.883	0.914
Mean AUC			0.887	0.902	0.917	0.913	0.934

ISSN: 1471-2164