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Table 2 Pattern discovery using ROMs (regions of overlapping matches) with maximal score to find binding sites in DNA

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

Regulatory protein Number of genes in the regulon* Touched by max Percent touched by max Touched by other§ Total percent touched Not touched** Without dyads††
ArgR 6 2 33.33 4 100.00 0 0
CRP 54 42 77.78 8 92.59 4 0
FNR 17 10 58.82 0 58.82 2 5
GlpR 4 3 75.00 1 100.00 0 0
IlvY 2 2 100.00 0 100.00 0 0
LexA 8 8 100.00 0 100.00 0 0
MalI 2 2 100.00 0 100.00 0 0
MalT 4 4 100.00 0 100.00 0 0
MelR 2 2 100.00 0 100.00 0 0
NR_I 3 3 100.00 0 100.00 0 0
NarL 6 3 50.00 0 50.00 2 1
PhoB 4 4 100.00 0 100.00 0 0
PurR 12 11 91.67 0 91.67 1 0
TorR 1 1 100.00 0 100.00 0 0
TrpR 5 4 80.00 1 100.00 0 0
TyrR 8 7 87.50 0 87.50 1 0
  1. *The total number of genes in the regulon with a known binding site (in the 400+50 upstream regions). The number of regions where a ROM (region of overlapping matches) with the highest number of matches (max ROM) touches a known binding site. This value expressed as a percentage. §Number of regions where either a ROM or dyad touches a known binding site, but the max ROM does not. The percentage of all upstream regions in which any ROM touches a binding site. **Number of regions with dyads, but no match between known binding sites and ROMs. ††Number of regions with no dyads at all.