Table 1.
Listeria monocytogenes genome sequences used in the Listeria GeneChip design.
Figure 1.
Effects of Tau values on gene present calls (LS402; A, LS406; B and LS411; C) and percent reproducibility (LS402; D, LS406; E and LS411; F).
Figure 2.
Effects of Tau values on percent false negative and positive calls based on the hybridization results of strain LS411.
Left axis indicates percent false positive (□) and false negative (Δ) Right axis indicates percent reproducibility (○) from the three LS411 hybridization results.
Figure 3.
Scatter plots of the summarized Robust Multi-array Averaging (RMA) intensities from the triplicate experiments of strains LS402 (A, B), LS406 (C, D), and LS411 (E, F).
Figure 4.
Comparison of the summarized Robust Multi-array Averaging (RMA) intensities by scatter plots.
Between strains from the same epidemic clones (ECIV) and pathotypes; FG, LS402 and LS406 (A) and Inv; LS415 and LS416 (B). Between strains from the same epidemic clones (ECI) and pathotype (Inv), different outbreaks; LS411 and LS413 (C). Between strains from the same epidemic clones (ECIV), different pathotype; Inv, LS415 and FG, LS406 (D). Red dots indicate summarized RMA intensity differences of less than or equal to 2-fold between two strains. Blue dots indicate RMA intensity differences of more than 2-fold between two strains.
Figure 5.
Hierarchical clustering dendrogram and heat map analysis based on the summarized Robust Multi-array Averaging (RMA) intensities obtained from all of the strains using in this study.
The RMA summarized probe-set intensities are ranging from 2.5 (green) to 14 (red).
Figure 6.
Relatedness analysis of the compatible parsimony informative genes from the 38 strains of L. monocytogenes.
The tree was generated from the concatenated gene contents using neighbor joining with the uncorrected p distance. The colors indicated the serotype of L. monocytogenes strains (red; serotype 4b, green; serotype 1/2b and blue; serotype 1/2a). Scale bar represents number of gene differences (present or absent) per gene site.
Figure 7.
A neighbor-net constructed from the gene contents from 31 strains belonging to the two serotypes 1/2b and 4b.
The parallel edges represent incompatible signals indicative of independent gene loss or gain due to the multiple transductions or recombinations. Serotypes and epidemic clones are grouped in different color as indicated. Node labels refer to strain names (Listed in Table S1). Scale bar represents number of gene differences (present or absent) per gene site.