Number of Controls Scoring Above Different Cutoffs
| Cutoffs | Motifs from E. coli controls | True positives | Additional real motifs | False positives | |||||
| MAP | S site | additional | |||||||
| 0 | 1 | (no cutoffs) | 591 | 26 (81%) | 5 | 95% | |||
| 5 | 1 | 299 | 22 (69%) | 5 | 91% | ||||
| 10 | 1 | 152 | 22 (69%) | 3 | 84% | ||||
| 5 | 1e-10 | 92 | 20 (63%) | 4 | 74% | ||||
| 10 | 1e-10 | 56 | 20 (63%) | 3 | 59% | ||||
| 10 | 1e-15 | 20 | 15 (47%) | 1 | 20% | ||||
| 10 | 1e-20 | 9 | 9 (28%) | 0 | 0% | ||||
| 10 | 1e-25 | 3 | 3 (9%) | 0 | 0% | ||||
| 10 | 1e-10 | pal | 10 | 8 (25%) | 2 | 0% | |||
| 10 | 1e-10 | pal, AT < 80 | 10 | 8 (25%) | 2 | 0% | |||
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↵Motifs where more than half of the aligned sites originate from a single input sequence were not included to eliminate repetitive elements. Minimum MAP score and maximum site specificity score (Ssite ) are indicated. “pal” means the motif is planidromic (CompareACE score to its reverse complement is >0.7). AT is the %AT content.
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↵Total number of different motifs found within eachE. coli regulon by aligning the upstream regions of known regulons in E. coli. Motifs found in the upstream regions of each regulon were clustered by similarity, and the total number of distinct motifs summed over all 32 regulons is given here.
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↵Percentage of 32 E. coli regulons with 5–100 known sites where the known regulatory motif can be found.
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↵Additional known motifs found due to overlap of regulons (i.e., the ArcA motif found upstream of the genes making up the Fnr regulon).
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↵Percentage of all motifs above this cutoff found in the upstream regions of footprinted regulons in E. coli, which are different from a motif known to regulate this groups of genes (CompareACE score greater than 0.7).
