Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification

Table 3 Accuracy of the pan-genome array for detecting genes and homologous groups

Chip Data	Test Data	Present	Absent	ACC	TPR	FPR	FDR
EGD-e	EGD-e genes only	2846	0	1.000 ± 0.000	1.000 ± 0.000	N/A	N/A
EGD-e	All gene variants	49068	2746	0.973 ± 0.002	0.973 ± 0.003	0.020 ± 0.009	0.001 ± 0.000
EGD-e	Gene groups	2642	918	0.989 ± 0.002	0.993 ± 0.001	0.024 ± 0.007	0.008 ± 0.003
EGD-e(-)	Gene groups	2627	918	0.987 ± 0.002	0.991 ± 0.001	0.024 ± 0.007	0.008 ± 0.003
J2-071	J2-071 genes only	2694	0	1.000	1.000	N/A	N/A
J2-071	All gene variants	47411	4403	0.964	0.970	0.090	0.009
J2-071	Gene groups	2543	1017	0.978	0.995	0.063	0.025
J2-071(-)	Gene groups	2468	1016	0.969	0.982	0.062	0.025

Present/Absent are based on a tblastn search. ACC, TPR, FPR, FDR stand for accuracy, true-positive rate, false-positive rate, and false discovery rate, respectively. (-) Excludes all probes directly targeting the hybridized strain from the analysis to simulate detection accuracy for an unknown strain. For EGD-e, the mean of 9 data sets are given, along with their standard deviation to illustrate array reproducibility.

ISSN: 1471-2164