Table 7.
Exons predicted by the programs not overlapping GENCODE annotated exons, and supported by transfrag evidence from genome tiling microarrays
| Total number of unique exons | Number of exons overlapping TARs/transfrags (%) | Number of non-annotated exons | Number of non-annotated exons overlapping TARs/transfrags (%) | Number of intergenic exons | Number of Intergenic exons overlapping TARs/transfrags (%) | |
| Category 1 | ||||||
| AUGUSTUS-any | 4,160 | 2,718 (65.3%) | 484 | 74 (15.3%) | 281 | 38 (13.5%) |
| FGENESH++ | 4,784 | 2,766 (57.8%) | 1,071 | 146 (13.6%) | 885 | 123 (13.9%) |
| JIGSAW | 3,935 | 2,673 (67.9%) | 206 | 34 (16.5%) | 130 | 19 (14.6%) |
| PAIRAGON-any | 4,414 | 3,080 (69.8%) | 284 | 84 (29.6%) | 221 | 68 (30.8%) |
| Category 2 | ||||||
| AUGUSTUS-abinit | 3,699 | 2,336 (63.2%) | 776 | 175 (22.6%) | 482 | 111 (23.0%) |
| GENEMARK.hmm | 6,897 | 2,552 (37.0%) | 3,796 | 319 (8.4%) | 2,826 | 244 (8.6%) |
| GENEZILLA | 3,415 | 1,535 (44.9%) | 1,361 | 110 (8.1%) | 970 | 69 (7.1%) |
| Category 3 | ||||||
| ACEVIEW | 8,410 | 5,756 (68.4%) | 539 | 118 (21.9%) | 449 | 106 (23.6%) |
| AUGUSTUS-EST | 4,073 | 2,700 (66.3%) | 439 | 73 (16.6%) | 253 | 37 (14.6%) |
| ENSEMBL | 4,505 | 3,094 (68.7%) | 251 | 27 (10.8%) | 187 | 17 (9.1%) |
| EXOGEAN | 5,014 | 3,480 (69.4%) | 183 | 21 (11.5%) | 100 | 15 (15.0%) |
| EXONHUNTER | 6,376 | 2,843 (44.6%) | 2,782 | 257 (9.2%) | 2,055 | 187 (9.1%) |
| PAIRAGON+NSCAN_EST 4,404 | 3,073 (69.8%) | 284 | 84 (29.6%) | 221 | 68 (30.8%) | |
| Category 4 | ||||||
| AUGUSTUS-dual | 4,024 | 2,588 (64.3%) | 629 | 114 (18.1%) | 364 | 65 (17.9%) |
| DOGFISH | 3,194 | 2,290 (71.7%) | 267 | 115 (43.1%) | 225 | 99 (44.0%) |
| MARS | 4,623 | 2,801 (60.6%) | 948 | 161 (17.0%) | 528 | 89 (16.9%) |
| NSCAN | 3,996 | 2,686 (67.2%) | 500 | 133 (26.6%) | 342 | 92 (26.9%) |
| SAGA | 2,115 | 1,147 (54.2%) | 564 | 36 (6.4%) | 433 | 26 (6.0%) |
| All unique exons (18 progs) | 26,818 | 12,001 (44.7%) | 12,025 | 1,563 (13.0%) | 8,634 | 1,163 (13.5%) |