Figure 2.

Comparison of gene essentiality predictions with TraSH data for in vitro growth on Middlebrook 7H10 medium. (a) Dependence of prediction results on the model and experimental thresholds for declaring gene essentiality. The plot shows receiver operating characteristic (ROC) curves for different transposon site hybridization (TraSH) ratio thresholds for determination of essential genes in experimental data. Each ROC curve shows 100 points corresponding to sensitivity and specificity of the model predictions obtained for growth rate thresholds varying in the range from 0.0 to 0.1 (increment 0.001). The growth rate threshold has little effect on prediction parameters. For values greater than 0.052 all genes were declared essential. Any threshold in the range from 0.001 to 0.041 resulted in exactly the same gene essentiality predictions. The ROC curve closest to the best theoretically possible prediction (sensitivity and specificity equal to 1) was obtained for a TraSH ratio threshold of 0.1. (b) Distributions of the hybridization ratio of the TraSH library to genomic DNA signal recorded in TraSH experiment for genes present in the model. Blue line shows distribution of the TraSH ratio among the genes that were predicted by the model to be essential for growth. Red line shows distribution of TraSH ratio among genes predicted to be nonessential for growth. Medians of the two distributions are significantly different by means of the Mann-Whitney test (P < 2 × 10^-16). Thus, the genes that are predicted to be essential have significantly lower median value of insertion probe to genomic probe ratio than genes predicted to be nonessential. This is in accordance with experimental data, because the low ratio indicates that inactivation of the target gene by transposon insert results in depletion of the mutant strain after the growth on Middlebrook 7H10 medium.