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Table 3 Distribution of differentially expressed (DE) bins among different genomic annotations

From: Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells

  3 hours 6 hours 12 hours 24 hours 48 hours
  Down-regulated* Up-regulated* Down-regulated* Up-regulated* Down-regulated* Up-regulated* Down-regulated* Up-regulated* Down-regulated* Up-regulated*
Total number of DE bins 8,316 17,348 4,107 6,746 5,276 5,264 6,714 5,464 6,217 3,939
Exonic bins 392 2,053 249 356 299 434 334 258 203 269
Bins that overlap both exons and introns 648 2,597 409 699 492 704 566 617 429 386
Bins that overlap Ensembl exons 127 297 79 92 79 110 101 104 72 58
Bins that overlap exons of Ensembl retained introns 27 78 29 26 24 20 31 32 25 25
Bins that overlap both Ensembl exons and exons of Ensembl retained introns 3 9 1 1 0 2 5 2 0 1
Intronic bins 6,530 10,274 3,041 5,063 4,062 3,515 5,359 3,995 5,070 2,953
Bins that overlap EST (both exons and introns) 75 223 41 65 57 71 50 53 65 46
Bins that overlap EST (exons only) 25 115 23 34 29 46 19 33 21 16
Bins that overlap EST (introns only) 248 527 73 123 86 96 95 99 91 56
Intergenic bins 241 1,175 162 287 148 266 154 271 241 129
Total number of DE bins 100.00 % 100.00 % 100.00 % 100.00 % 100.00 % 100.00 % 100.00 % 100.00 % 100.00 % 100.00 %
Exonic bins 4.71 % 11.83 % 6.06 % 5.28 % 5.67 % 8.24 % 4.97 % 4.72 % 3.27 % 6.83 %
Bins that overlap both exons and introns 7.79 % 14.97 % 9.96 % 10.36 % 9.33 % 13.37 % 8.43 % 11.29 % 6.90 % 9.80 %
Bins that overlap Ensembl exons 1.53 % 1.71 % 1.92 % 1.36 % 1.50 % 2.09 % 1.50 % 1.90 % 1.16 % 1.47 %
Bins that overlap exons of Ensembl retained introns 0.32 % 0.45 % 0.71 % 0.39 % 0.45 % 0.38 % 0.46 % 0.59 % 0.40 % 0.63 %
Bins that overlap both Ensembl exons and exons of Ensembl retained introns 0.04 % 0.05 % 0.02 % 0.01 % 0.00 % 0.04 % 0.07 % 0.04 % 0.00 % 0.03 %
Intronic bins 78.52 % 59.22 % 74.04 % 75.05 % 76.99 % 66.77 % 79.82 % 73.11 % 81.55 % 74.97 %
Bins that overlap EST (both exons and introns) 0.90 % 1.29 % 1.00 % 0.96 % 1.08 % 1.35 % 0.74 % 0.97 % 1.05 % 1.17 %
Bins that overlap EST (exons only) 0.30 % 0.66 % 0.56 % 0.50 % 0.55 % 0.87 % 0.28 % 0.60 % 0.34 % 0.41 %
Bins that overlap EST (introns only) 2.98 % 3.04 % 1.78 % 1.82 % 1.63 % 1.82 % 1.41 % 1.81 % 1.46 % 1.42 %
Intergenic bins 2.90 % 6.77 % 3.94 % 4.25 % 2.81 % 5.05 % 2.29 % 4.96 % 3.88 % 3.27 %
  1. *Relative to the control time point.