Table 4.
Phylogenetic Footprinting Results for the Study Set Using Orthologous Data from Multiple Species
| Number of motif predictions | Correspondence with known sites | Motif predictions with avg MAP ≥ critical value | Correspondence with known sites for: | ||||||
| Motif predictions with avg MAP ≥ critical value | Motif predictions with avg MAP < critical value | ||||||||
| EC-ST-YP-VC-HI-SO-PA: | |||||||||
| Predictions with ≥2 species | 163 | 68.7% (112/163) | 52.1% (85/163) | 75.3% (64/85) | 61.5% (48/78) | ||||
| Predictions with ≥3 species | 116 | 74.1% (86/116) | 60.3% (70/116) | 80.0% (56/70) | 65.2% (30/46) | ||||
| Predictions with ≥4 species | 84 | 75.0% (63/84) | 69.0% (58/84) | 79.3% (46/58) | 65.4% (17/26) | ||||
| EC-YP-VC-HI-SO-PA: | |||||||||
| Predictions with ≥2 species | 140 | 67.9% (95/140) | 53.6% (75/140) | 84.0% (63/75) | 49.2% (32/65) | ||||
| Predictions with ≥3 species | 102 | 65.7% (67/102) | 60.8% (62/102) | 85.5% (53/62) | 35.0% (14/40) | ||||
| Predictions with ≥4 species | 65 | 69.2% (45/65) | 69.2% (45/65) | 84.4% (38/45) | 35.0% (7/20) | ||||
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MAP indicates maximum a posteriori probability; EC,Escherichia coli; ST, Salmonella typhi; YP,Yersinia pestis; VC, Vibrio cholerae; HI,Haemophilus influenzae; SO, Shewanella oneidensis; PA, Pseudomonas aeruginosa; BU,Buchnera sp.; AF, Acidithiobacillus ferrooxidans;and XF, Xylella fastidiosa.
