Table 3. Statistics for the gene essentiality prediction.

	Comparison with Glass et al (2006)	Comparison with Glass et al (2006) and mutants	Taking conditions into account
TP (true positive)	72	72	72
TN (true negative)	41	48	53
FP (false positive)	1	1	1
FN (false negative)	17	10	5
ACC (prediction accuracy)	0.8626	0.9160	0.9542
SPC (prediction specificity)	0.9762	0.9796	0.9815
ACC in %	86.26	91.60	95.42
SPC in %	97.62	97.96	98.15

The gene essentiality prediction for 131 metabolic genes has been evaluated (i) based on a genome-wide transposon study in M. genitalium (Glass et al, 2006), (ii) also taking into account single transposon screens in M. pneumoniae, and (iii) in addition, taking into account simulation conditions and biomass assumptions (for details, see Supplementary information). Italic ACC & SPC in % highlight the numbers referred to throughout the text.

TP—essential in vivo and in silico, TN—not essential in vivo and in silico, FP—essential in silico, not essential in vivo, FN—essential in vivo, not essential in silico.