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Table 2 Sensitivity and specificity of each method at detecting the 1,556 consensus transcripts

From: AceView: a comprehensive cDNA-supported gene and transcripts annotation

Track Number of models with introns Consensual models (of 1,556 total) Sensitivity Specificity
*AceView 1,792 1,302 84% 73%
Gencode 1,691 1,255 81% 74%
*ECgene 3,851 1,198 77% 31%
AceView 1,630 1,165 75% 71%
*ExonWalk 892 511 33% 57%
*Known Gene 501 432 28% 86%
Exogean 554 404 26% 73%
*RefSeq 342 332 21% 97%
Pairagon 471 310 20% 66%
*Ensembl 427 295 19% 69%
*MGC 323 217 14% 67%
Fgenesh 462 217 14% 47%
*P CCDS 201 152 10% 76%
UP Jigsaw 259 150 10% 58%
*U NscanEst 282 104 7% 37%
UP Augustus 312 100 6% 32%
P Twinscan 547 77 5% 14%
UP GeneMark 551 50 3% 9%
UP SGP2 552 48 3% 9%
UP GeneZilla 477 47 3% 10%
UP ExonHunter 807 41 3% 5%
UP GeneID 267 38 2% 14%
*UP GenScan 395 37 2% 9%
UP Dogfish 204 33 2% 16%
UP Saga 331 18 1% 5%
  1. Sensitivity and specificity of each method at detecting the 1,556 consensus transcripts across the pool of the following evidence based tracks: RefSeq, Known Gene, Ensembl, Gencode, AceView, ECgene and ExonWalk, as in Figure 3a. Coded information has been added in front of the track name: asterisks distinguish standard gene tracks, available genome-wide, from an ENCODE only track; a U track predicts a unique model per gene; P predicts protein coding regions only.