Table 1

Alternative splicing events

AS

AS events


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.

Rogers et al. Genome Biology 2012 13:R4   doi:10.1186/gb-2012-13-1-r4

Open Data