Table 3.

A survey of alternative exon splicing events identified with MapSplice junctions

Coverage	Alternative exon events				Mutual Excl.
	Sample	Skipped Exon	Alt. Start	Alt. End
1	BAS	6880	6700	7474	442
	BAS	7365	7611	8005	454
	SUM	5574	5690	6359	353
	SUM	5491	5701	6451	337
	LUM	6523	7326	7777	387
	LUM	6321	6928	7625	355
	MCF	6776	6338	7350	472
	MCF	6352	6063	7083	444
2	BAS	2726	2144	2564	101
	BAS	2941	2529	2689	111
	SUM	2271	2098	2347	103
	SUM	2277	2096	2359	95
	LUM	2599	2542	2574	95
	LUM	2333	2031	2387	86
	MCF	2949	2410	2778	129
	MCF	2669	2331	2588	109
5	BAS	651	476	614	26
	BAS	718	522	641	23
	SUM	644	538	643	25
	SUM	623	528	656	25
	LUM	618	538	582	22
	LUM	503	386	528	21
	MCF	815	686	780	30
	MCF	757	656	735	22

Four different types of alternative splicing events involving at least two splice junctions were identified in each sample. They are exon skipping events, alternative 3′-end, alternative 5′ start and mutually exclusive exons. Alternative splicing events were examined at different expression levels, only junctions with coverage larger than the given threshold (1, 2, 5) were considered. In general, there are about 35% exon skipping events, 30% alternative 5′ start events, 34% alternative 3′-end events and 1.3% mutually exclusive exon events.