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Table 4 Motif similarity between the first and second promoters of the same genea

From: Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster

  Similarb Intermediateb Differentb # of used pairs # of omitted pairs
  allc high qualityd cape all high quality cap all high quality cap all high quality cap all high quality cap
Observed value (shared motifs allowed) 34.07 31.52 36.04 17.70 16.30 23.42 48.23 52.17 40.54 226 92 111 1182 445 278
Observed value (shared motifs not allowed) 12.65 11.59 15.19 15.66 15.94 21.52 71.69 72.46 63.29 166 69 79 1242 468 310
Random meanf 9.50 8.34 8.67 10.83 12.51 14.31 79.66 79.15 77.03 226 92 111 1182 445 278
p-valueg (random >= observed value, shared motifs allowed) 0 0 0 2e-04 0.1399 0.0021 1 1 1 -- -- -- -- -- --
p-valueg (random <= observed value, shared motifs allowed) 1 1 1 1 0.9227 0.9991 0 0 0 -- -- -- -- -- --
p-valueg (random >= observed value, shared motifs not allowed) 0.0438 0.1286 0.0078 0.0041 0.1399 0.0108 0.9991 0.9622 1 -- -- -- -- -- --
p-valueg (random <= observed value, shared motifs not allowed) 0.9562 0.8714 0.9922 0.9959 0.8601 0.9892 9e-04 0.0378 0 -- -- -- -- -- --
  1. agenes with exactly two alternative promoters. Similar results were obtained for genes with multiple alternative promoters (data not shown).
  2. bpercentage of the alternative promoter pairs defined as similar, intermediate, and different (see Methods).
  3. cThe promoter set contains all promoters from Drosophila genome annotation release 5.5.
  4. dThe promoter set contains only high quality promoters in fly genome; see Methods.
  5. eThe promoter set contains only cap-supported promoters in fly genome; see Methods.
  6. fmean of 10,000 randomizations.
  7. gempirical p-value calculated as the proportion of sampled randomizations where the percentage of the promoter pairs in each of the three similarity levels was no less than/no greater than the observed values