Whole genome transcriptome polymorphisms in Arabidopsis thaliana

Table 1 Differential spliced exons and introns detected at different thresholds

	Delta*	Sig+^†	Sig-^†	Total	False^‡	FDR (%)
Exon (gene mean)^§	0.3	287	190	477	559	117
	0.4	177	129	306	205	67.0
	0.5	127	109	236	97	41.0
	0.6	92	86	178	55	30.8
	0.7	77	69	146	34	23.4
	0.8	57	54	111	23	20.8
	0.9	32	39	71	16	22.8
	1	28	29	57	12	20.5
Exon (gene median)^¶	0.3	523	280	803	556	69.2
	0.4	328	172	500	203	40.6
	0.5	223	120	343	96	28.0
	0.6	154	76	230	54	23.5
	0.7	123	52	175	34	19.3
	0.8	101	47	148	23	15.6
	0.9	71	32	103	16	15.6
	1	56	28	84	12	13.8
Exon (splicing index)^¥	0.3	402	249	651	302	46.4
	0.4	310	172	482	86	17.8
	0.5	233	132	365	30	8.16
	0.6	166	92	258	12	4.64
	0.7	134	86	220	6	2.53
	0.8	105	74	179	3	1.56
	0.9	80	60	140	2	1.16
	1	64	50	114	1	0.77
Intron	0.3	561	1,034	1,595	332	20.8
	0.4	405	523	928	85	9.17
	0.5	316	352	668	28	4.26
	0.6	239	220	459	12	2.61
	0.7	202	155	357	7	1.91
	0.8	176	120	296	5	1.53
	0.9	140	94	234	3	1.31
	1	120	75	195	2	1.15

The total number of analyzed exons was 68,022 for 15,349 genes, and of analyzed introns was 62,859 for17,434 genes. *Thresholds. ^†Significant calls with greater expression in Col (Sig+) or greater expression in Van (Sig-). ^‡False calls based on 1,000 permutations. ^§Exonic splicing analysis using exon intensity corrected by gene mean. ^¶Exonic splicing analysis using exon intensity corrected by gene median. ^¥Exonic splicing analysis using splicing index.

ISSN: 1474-760X