Stepwise approach for combining many sources of evidence for site-recognition in genomic sequences

Pérez-Rodríguez, Javier; García-Pedrajas, Nicolás

doi:10.1186/s12859-016-0968-y

BMC Bioinformatics

Table 7 The table shows the specificity (Sp), sensitivity (Sn), true positives (TP), true negatives (TN), false negatives (FN), false positives (FP) and area under the ROC and PRC curves (auROC/PRC) as well as the time needed for obtaining the best combination for all methods and the five studied chromosomes for stop codon recognition

From: Stepwise approach for combining many sources of evidence for site-recognition in genomic sequences

Chromosome	Objective	Method	Combination	auROC	auPRC	G	Sp	Sn	TP	FN	TN	FP	#models	Time(s)
Chr. 1	-	Std	-	0.9280	0.0142	0.8487	0.8942	0.8055	1735	419	21,077,932	2,495,099	-	-
	auROC	Cons	Sum	0.9705	0.0368	0.8868	0.9707	0.8101	1745	409	22,882,052	690,979	4	4818
	auPRC	Cons	Sum	0.9522	0.0525	0.8165	0.9762	0.6829	1471	683	23,011,801	561,230	22	9702
	G	Cons	Majority	0.9307	0.0013	0.9207	0.9426	0.8993	1937	217	22,218,892	1,354,139	2	1223
Chr. 3	-	Std	-	0.9233	0.0083	0.8256	0.9159	0.7442	829	285	19,711,889	1,810,611	-	-
	auROC	Cons	Sum	0.9720	0.0262	0.8959	0.9676	0.8294	924	190	20,826,101	696,399	4	4,094
	auPRC	Cons	Sum	0.9421	0.0297	0.7810	0.9735	0.6266	698	416	20,951,286	571,214	10	8019
	G	Cons	Majority	0.9584	0.0015	0.9128	0.9462	0.8806	981	133	20,364,397	1,158,103	4	1719
Chr. 13	-	Std	-	0.9185	0.0071	0.8150	0.9103	0.7297	243	90	9,902,079	976,223	-	-
	auROC	Cons	Sum	0.9585	0.0156	0.8817	0.9733	0.7988	266	67	10,587,495	290,807	5	4542
	auPRC	Cons	Sum	0.9392	0.0311	0.7604	0.9824	0.5886	196	137	10,687,114	191,188	20	9136
	G	Cons	Majority	0.9502	0.0106	0.8878	0.9545	0.8258	275	58	10,383,296	495,006	6	1619
Chr. 19	-	Std	-	0.9328	0.0379	0.8515	0.8664	0.8368	1190	232	4,042,574	623,230	-	-
	auROC	Cons	Sum	0.9731	0.0843	0.9160	0.9335	0.8987	1278	144	4,355,655	310,149	5	3878
	auPRC	Cons	Sum	0.9557	0.1119	0.8787	0.9250	0.8347	1187	235	4,316,077	349,727	15	8806
	G	Cons	Majority	0.9346	0.0026	0.9169	0.9002	0.9339	1328	94	4,199,984	465,820	2	856
Chr. 21	-	Std	-	0.8890	0.0083	0.7778	0.9191	0.6582	156	81	3,425,375	301,584	-
	auROC	Cons	Sum	0.9674	0.0383	0.8797	0.9654	0.8017	190	47	3,597,983	128,976	4	2379
	auPRC	Cons	Sum	0.9455	0.0382	0.7970	0.9713	0.6540	155	82	3,620,079	106,880	18	8134
	G	Cons	Majority	0.9199	0.0007	0.9087	0.9320	0.8861	210	27	3,473,463	253,496	2	507

The results of our method for the three different evaluation measures are shown in boldface

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