Table 1 |
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|
Alternative splicing events |
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|
AS |
AS events |
|||||
|
|
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|
genes |
IR |
ES |
Alt. 5' |
Alt. 3' |
Total |
|
|
|
||||||
|
A. thaliana models |
4,029 |
1,987 (33%) |
550 (9%) |
1,256 (21%) |
2,145 (36%) |
5,938 |
|
SpliceGrapher |
||||||
|
No ESTs |
4,901 |
2,248 (30%) |
714 (10%) |
1,560 (21%) |
2,866 (39%) |
7,388 |
|
Novel |
885 |
308 (21%) |
164 (11%) |
304 (20%) |
721 (48%) |
1,497 |
|
With ESTs |
6,162 |
3,658 (33%) |
994 (9%) |
2,335 (21%) |
4,128 (37%) |
9,916 |
|
Novel |
2,154 |
1,779 (34%) |
444 (8%) |
1,079 (20%) |
1,983 (38%) |
5,285 |
|
Cufflinks |
||||||
|
No gene models |
1,263 |
449 (32%) |
383 (28%) |
237 (17%) |
319 (23%) |
1,388 |
|
Novel |
699 |
429 (32%) |
380 (28%) |
232 (17%) |
304 (23%) |
1,345 |
|
With gene models |
6,056 |
4,029 (39%) |
2,857 (27%) |
1,427 (14%) |
2,106 (20%) |
10,419 |
|
Novel |
2,319 |
2,232 (38%) |
2,550 (43%) |
552 (9%) |
594 (10%) |
5,928 |
|
TAU |
||||||
|
No gene models |
2,777 |
893 (17%) |
475 (9%) |
1,481 (27%) |
2,555 (47%) |
5,404 |
|
Novel |
1,591 |
811 (16%) |
460 (9%) |
1,431 (28%) |
2,351 (47%) |
5,053 |
|
With gene models |
10,458 |
94,571 (85%) |
598 (1%) |
5,972 (5%) |
9,820 (9%) |
110,961 |
|
Novel |
8,364 |
94,124 (86%) |
476 (0%) |
5,697 (5%) |
9,219 (8%) |
109,516 |
|
V. vinifera models |
0 |
0 (0%) |
0 (0%) |
0 (0%) |
0 (0%) |
0 |
|
SpliceGrapher |
2,039 |
347 (13%) |
830 (31%) |
640 (24%) |
838 (32%) |
2,655 |
|
TAU |
||||||
|
No gene models |
3,099 |
531 (10%) |
684 (13%) |
1,321 (25%) |
2,743 (52%) |
5,279 |
|
With gene models |
15,874 |
135,585 (72%) |
4,938 (3%) |
23,615 (13%) |
24,406 (13%) |
188,544 |
|
Cufflinks |
||||||
|
No gene models |
1,057 |
324 (24%) |
519 (39%) |
140 (11%) |
349 (26%) |
1,332 |
|
With gene models |
4,263 |
4,120 (34%) |
3,148 (26%) |
2,165 (18%) |
2,818 (23%) |
12,251 |
|
|
||||||
|
The number of AS events detected by SpliceGrapher, Cufflinks, and TAU compared with events inferred from the TAIR9 annotations. We track the following AS event types: intron retention (IR), exon skipping (ES), alternative 5' sites (Alt. 5') and alternative 3' sites (Alt. 3'). SpliceGrapher uses the TAIR9 gene models as a baseline, so it includes all of the same AS events along with additional events inferred from RNA-Seq data. Without gene models, nearly all TAU and Cufflinks predictions are novel AS events. With gene models, more than half of Cufflinks predictions reproduce AS events from the gene models. TAU uses known splice sites to predict all possible exons in a gene, generating vast numbers of novel exons and novel IR events. |
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|
Rogers et al. Genome Biology 2012 13:R4 doi:10.1186/gb-2012-13-1-r4 |
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