Skip to main content

Table 2 Dataset for evaluating tag assignment

From: Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data

Dataset Subset Total w/o Tagsa w/Tags Hitsb %
cDNA cDNA 2480 0 2480 2480 100
Unigenec Unigene 2806 3 2803 2627 93.62
  Uni-S 2712 1 2711 2598 95.80
  Uni-N 94 1 93 29 30.85
  UniBest 2480 0 2480 2414 97.34
  Max-Length 2480 0 2480 2411 97.22
ESTc EST 54764 3597 51167 36484 66.62
  EST-S 26242 1631 24611 18788 71.60
  EST-A 2749 182 2567 1665 60.57
  EST-N 21169 1592 19577 12702 60.00
  EST-B 4604 192 4412 3329 72.31
  ESTBest 2480 19 2461 1842 74.27
  Max-Length 2480 19 2461 1858 74.92
Predictedd Predicted 2480 44 2436 415 16.73
  P-100 2480 26 2454 787 31.73
  P-200 2480 9 2471 1308 52.74
  P-300 2480 4 2476 1457 58.75
  P-400 2480 2 2478 1181 47.62
  P-500 2480 1 2479 869 35.04
  1. a Numbers of cDNA sequences that do not have tags due to the absence of NlaIII sites. b Numbers of virtual tags that matched to our empirical dataset. c Capital letters stand for transcripts that have 3' polyA signal (S), 3' polyA tail (A), both the signal and the tail (B), and neither (N), respectively. d Predicated gene models and extended lengths (bp) from stop codon (P-100 to P-500).