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Table 1 Alternative splicing events

From: SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

  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
  1. 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.