Skip to main content

Advertisement

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

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

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
  1. 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.