Supplementary data

Case study I : Five plant species comparative performance between cncRNADetector:

Data set	Tools	TP	FP	TN	FN	SE	SPC	PPV	NPV	F1 score	MCC	ACC
Sorghum bicolor (4541 lncRNA) (4541 mRNA)	cncRNADetector	4161	692	3849	380	91.63	84.76	85.74	91.01	88.89	76.57	88.20
	CPC	3791	892	3849	750	83.48	84.76	84.56	83.69	84.02	68.25	84.12
	CPC2	4027	597	3944	469	89.57	86.85	87.09	89.37	88.31	76.44	88.20
	LGC	4085	813	3729	496	89.19	82.10	83.40	88.26	86.19	71.46	85.65
	PLEK	3626	1225	3316	915	79.85	73.02	74.75	78.37	77.21	63.00	76.44
Zea mays (12071 lncRNA) (12071 mRNA)	cncRNADetector	10911	2035	10036	1160	90.39	83.14	84.28	89.64	87.23	73.73	86.77
	CPC	10612	1757	10314	1459	87.91	83.10	84.56	87.61	86.84	73.38	86.68
	CPC2	10592	2053	10018	1479	87.75	82.99	87.09	87.17	85.71	70.82	85.37
	LGC	10848	2764	9307	1223	89.87	77.10	83.40	88.39	84.48	67.52	83.49
	PLEK	11207	4497	7574	864	92.84	62.75	74.75	89.76	80.70	58.29	77.79
Brachypodium distachyon (4868 lncRNA) (4868 mRNA)	cncRNADetector	4374	780	4088	494	89.85	83.98	84.87	89.22	87.29	73.96	86.91
	CPC	4025	791	4077	843	82.68	83.75	73.58	82.87	83.13	66.44	83.22
	CPC2	4313	665	4203	555	88.60	86.34	86.64	88.34	87.61	74.96	87.47
	LGC	4377	885	3983	491	89.91	81.82	83.18	89.03	86.42	71.97	85.87
	PLEK	4082	1449	3419	786	83.85	70.23	73.80	81.31	78.51	54.60	77.04
Manihot esculenta (3017 lncRNA) (3017 mRNA)	cncRNADetector	2519	0	3017	498	83.49	100	100	85.83	91.00	94.65	91.75
	CPC	2380	308	2709	637	78.89	89.79	88.54	80.96	83.44	69.09	84.34
	CPC2	2646	333	2684	371	87.70	88.96	88.80	87.86	88.26	76.67	88.33
	LGC	2347	364	2653	670	77.79	87.94	86.57	79.84	81.95	66.07	82.86
	PLEK	2849	1153	1864	168	94.43	61.78	71.19	91.73	81.18	59.47	78.11
Arabidopsis thaliana (2517 lncRNA) (2517 mRNA)	cncRNADetector	2512	386	2131	5	99.80	84.66	86.68	99.77	92.78	85.45	92.23
	CPC	2498	399	2118	19	99.25	84.15	86.23	99.11	92.28	84.36	91.70
	CPC2	2508	401	2118	9	99.64	84.07	86.22	99.58	92.44	84.74	91.86
	LGC	2494	390	2116	23	99.09	84.51	86.48	98.93	92.35	84.49	91.80
	PLEK	2505	1079	1438	12	99.52	57.13	69.89	99.17	82.12	62.55	78.33

Case study II : Evaluation of cncRNADetector with real-world cases.:

EXPERIMENTALLY VALIDATED lncRNAs dataset	TOOLS	TP	FP	SE
BD-21 EST (858)	cncRNADetector	858	0	100
	CNIT	389	469	45.33
	LGC	857	1	99.88
	PLEK	848	10	98.83
	CPC	856	2	99.76
	CPC2	855	3	99.65
BD-21 (5851)	cncRNADetector	5683	168	97.12
	CNIT	4579	1272	78.26
	LGC	5651	200	96.58
	PLEK	5542	309	94.71
	CPC	5681	170	97.09
	CPC2	5684	167	97.14
Populus tomentosa (set 1) (875)	cncRNADetector	875	0	100
	CNIT	720	155	82.28
	LGC	861	14	98.40
	PLEK	825	50	94.28
	CPC	5681	5	99.42
	CPC2	5684	2	99.77
Populus tomentosa (set 2) (355)	cncRNADetector	346	9	97.46
	CNIT	334	21	94.08
	LGC	348	7	98.14
	PLEK	348	7	98.06
	CPC	343	12	96.90
	CPC2	349	6	98.45
Gossypium barbadense (3400)	cncRNADetector	3390	10	99.70
	CNIT	3160	240	92.94
	LGC	3355	45	98.67
	PLEK	3016	384	88.70
	CPC	3387	13	99.61
	CPC2	3384	16	99.52
EVLncRNAs 2.0 (277)	cncRNADetector	269	8	97.11
	CNIT	229	48	82.67
	LGC	268	9	96.75
	PLEK	199	78	71.84
	CPC	262	15	94.58
	CPC2	269	8	97.11
PncStress (661)	cncRNADetector	639	22	96.67
	CNIT	612	49	92.58
	LGC	635	26	96.06
	PLEK	542	19	81.99
	CPC	628	33	95.00
	CPC2	642	19	97.12
PlncDB (6132)	cncRNADetector	5282	851	86.12
	CNIT	5129	1003	83.64
	LGC	4970	1162	81.05
	PLEK	4822	1210	78.63
	CPC	4912	1310	78.63
	CPC2	5138	994	83.78
EnSembl_plants (12022)	cncRNADetector	11856	166	98.61
	CNIT	9129	2893	75.93
	LGC	11012	1010	91.59
	PLEK	7119	4903	59.21
	CPC	10286	1733	85.55
	CPC2	11813	209	98.26

Task

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