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Table 4 Pattern discovery at the level of binding sites

From: Evaluation of thresholds for the detection of binding sites for regulatory proteins in Escherichia coliK12 DNA

  Consensus/Patser Dyad-analysis/sweeping
Regulon Sites/sites 250/sites 450/sites Sites/sites 250/sites 450/sites
AraC 100.00 8.33 8.33 58.33 - 41.67
ArcA 76.47 76.47 47.06 76.47 - 76.47
ArgR 75.00 58.33 58.33 100.00 16.67 50.00
CRP 90.53 87.37 88.42 66.32 46.32 47.37
CysB 100.00 42.86 28.57 - - -
CytR 100.00 12.50 12.50 - - -
FIS 55.56 66.67 - - - -
FNR 93.10 65.52 51.72 58.62 41.38 41.38
FadR 83.33 50.00 - - - -
FruR 100.00 14.29 71.43 71.43 - -
Fur 100.00 66.67 11.11 77.78 - -
GlpR 60.00 40.00 40.00 80.00 33.33 46.67
IHF 72.22 66.67 22.22 50.00 - -
LexA 100.00 88.89 88.89 100.00 100.00 100.00
Lrp 78.95 47.37 26.32 36.84 - -
MalT 66.67 22.22 22.22 55.56 44.44 77.78
NR_I 77.78 55.56 55.56 77.78 77.78 77.78
NagC 57.14 14.29 14.29 - - 28.57
NarL 75.00 35.00 15.00 55.00 - -
OmpR 71.43 - 7.14 42.86 - -
OxyR 75.00 25.00 - - - -
PhoB 71.43 57.14 57.14 71.43 71.43 42.86
PurR 92.86 85.71 78.57 92.86 78.57 85.71
TrpR 100.00 100.00 100.00 100.00 100.00 100.00
TyrR 86.67 73.33 66.67 53.33 46.67 60.00
Average 88.59 60.36 53.07 75.19 70.76 65.64
  1. For each family, we show the results of applying Dyad-analysis/sweeping and Consensus/Patser to the problem of discovering binding sites. The results contain pattern discovery data similar to those in Table 3, but this time counting the number of binding sites found per total number of sites. Again, only dyads extracted from max ROMs are used. The names of columns are as described in Table 3.