Table 1 The microorganisms and media conditions used in the study, together with the predicted gene essentiality results. The percentage of essential genes predicted correctly is a measure of how effective a screen the computational gene essentiality prediction really is.
From: Three factors underlying incorrect in silico predictions of essential metabolic genes
| Organism | Total # of genes | Experimental media | # of TP genes | # of FN genes | % essential genes correct |
|---|---|---|---|---|---|
| E. coli | 1261 | glucose MM | 157 | 81 | 66.0 |
| glycerol MM | 156 | 86 | 64.5 | ||
| S. cerevisiae | 750 | glucose | 63 | 95 | 39.9 |
| glucose (anaerobic) | 47 | 109 | 30.1 | ||
| galactose | 66 | 136 | 32.7 | ||
| glycerol | 66 | 132 | 33.3 | ||
| ethanol | 90 | 120 | 42.9 | ||
| rich | 28 | 90 | 23.7 | ||
| H. pylori | 339 | rich | 36 | 39 | 48.0 |
| S. aureus | 619 | rich (Forsyth et al.) | 7 | 27 | 20.6 |
| rich (Ji et al.) | 1 | 5 | 16.7 | ||
| M. tuberculosis | 661 | Middlebrook | 105 | 132 | 44.3 |
| B. subtilis | 844 | rich | 65 | 31 | 67.7 |
