Table 5 Mapping of experimental yeast SAGE-tags against the HGA-based annotation
From: Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression
Varela [17] | Velculescu [15] | Kal [16] | ||||
|---|---|---|---|---|---|---|
Frequency | Percentage | Frequency | Percentage | Frequency | Percentage | |
Classes | ||||||
Platinum (Pt) | 884 | 69.44 | 2,187 | 72.88 | 993 | 75.17 |
Gold (Au) | 54 | 4.24 | 134 | 4.47 | 68 | 5.15 |
Silver (Ag) | 5 | 0.39 | 12 | 0.40 | 5 | 0.38 |
Aluminum (Al) | 112 | 8.80 | 255 | 8.50 | 139 | 10.52 |
Copper (Cu) | 183 | 14.38 | 304 | 10.13 | 82 | 6.21 |
Iron (Fe) | 26 | 2.04 | 75 | 2.50 | 23 | 1.74 |
Silicon (Si) | 9 | 0.71 | 34 | 1.13 | 11 | 0.83 |
Confidences | ||||||
High | 1,177 | 92.46 | 2,756 | 91.84 | 1,204 | 91.14 |
Undefined | 96 | 7.54 | 245 | 8.16 | 117 | 8.86 |
Transcript context | ||||||
UTR-5' | 15 | 1.52 | 29 | 1.19 | 14 | 1.26 |
ORF (CDS) | 574 | 58.16 | 1,699 | 69.80 | 693 | 62.15 |
UTR-3' | 398 | 40.32 | 706 | 29.01 | 408 | 36.59 |
Intergenic and transcripts | ||||||
Intergenic | 218 | 17.12 | 413 | 13.76 | 116 | 8.78 |
Transcript opposite | 140 | 11.00 | 250 | 8.33 | 60 | 4.54 |
Transcript full | 1,041 | 81.78 | 2,561 | 85.34 | 1,188 | 89.93 |
Partial transcript | 14 | 1.10 | 27 | 0.90 | 17 | 1.29 |
Total transcripts | 1,055 | 82.88 | 2,588 | 86.24 | 1,205 | 91.22 |
Introns | ||||||
Intron | 6 | 0.61 | 5 | 0.21 | 1 | 0.09 |
Poly(A) next | ||||||
Poly(A) next | 70 | 7.09 | 189 | 7.76 | 73 | 6.55 |
Non coding RNAs | ||||||
Non-mRNAs | 12 | 1.22 | 7 | 0.29 | 4 | 0.30 |
Splicing | ||||||
Spliced | 1 | 0.08 | 1 | 0.03 | 4 | 0.30 |
Total | ||||||
Total | 1,273 | 100.00 | 3,001 | 100.00 | 1,321 | 100.00 |