Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems

Table 1 Area under the ROC curve (AUC) and relative ranking measured under all simulation studies

	Cufflinks	DEXSeq	MATS	SpComp	DSGseq	rDiff-param	DiffSplice	SeqGSEA
${High}_{100x}^{Diff}$	0.7765(3)	0.8435(1)	0.6066(7)	0.603(6)	0.8214(2)	0.704(5)	0.5262(8)	0.7699(4)
${Medium}_{100x}^{Diff}$	0.7334(3)	0.7583(1)	0.5960(6)	0.5612(7)	0.7472(2)	0.6421(5)	0.5276(8)	0.7055(4)
${Low}_{100x}^{Diff}$	0.6369(1)	0.5847(4)	0.5583(6)	0.518(7)	0.6288(2)	0.5807(5)	0.4982(8)	0.6155(3)
${High}_{100x}^{Same}$	0.7751(4)	0.8351(2)	0.6046(6)	0.5998(7)	0.8373(1)	0.6871(5)	0.5371(8)	0.7797(3)
${Medium}_{100x}^{Same}$	0.7357(4)	0.7407(2)	0.5914(6)	0.5582(7)	0.7669(1)	0.6201(5)	0.5341(8)	0.7374(3)
${Low}_{100x}^{Same}$	0.6487(2)	0.5546(5)	0.5506(6)	0.5159(7)	0.6496(1)	0.5773(4)	0.5049(8)	0.6297(3)
${100x}_{High}^{Diff}$	0.7765(3)	0.8435(1)	0.6066(7)	0.603(6)	0.8214(2)	0.704(5)	0.5262(8)	0.7699(4)
${60x}_{High}^{Diff}$	0.8687(1)	0.7667(2)	0.5861(6)	0.5688(7)	0.7648(3)	0.6848(5)	0.5266(8)	0.7338(4)
${25x}_{High}^{Diff}$	0.6807(4)	0.7432(1)	0.5607(6)	0.5479(7)	0.6967(2)	0.6659(5)	0.5001(8)	0.6815(3)
Complete annot.	0.7765(3)	0.8435(1)	0.6066(7)	0.603(6)	0.8214(2)	0.704(5)	0.5262 (8)	0.7699 (4)
Incomplete annot.	0.7271(1)	0.5939(5)	0.5012(8)	0.5930(6)	0.7033(2)	0.6561(3)	0.5262 (7)	0.6425 (4)
A3A5SS	0.8990(1)	0.8574(3)	0.8948(2)	0.5283(7)	0.6272(5)	0.5732(6)	0.4811(8)	0.6932(4)
IR	0.8810(4)	0.9368(1)	0.9360(2)	0.5639(8)	0.8990(3)	0.6696(6)	0.6391(7)	0.7940(5)
SE	0.8795(3)	0.9407(1)	0.9177(2)	0.7500(6)	0.8301(5)	0.5916(7)	0(8)	0.8334(4)
8samples	0.7408(5)	0.8495(1)	0.6078(7)	0.7450(4)	0.8301(2)	0.7196(6)	0.5030(8)	0.7656(3)

Larger values of AUC indicate better performance. The table contains the AUC and relative ranking for the methods under all simulation study. The best method under each study is highlighted in boldface. The ranking position is shown in the parenthesis. A3A5SS stands for the joint class of alternative 3’ splice site event and alternative 5’ splice site event. IR stands for intron retention event and SE stands for skipping exon event.

ISSN: 1471-2105