Supplementary Material
Additional file 1
List of the 254 genes of Helicobacter pylori strain 26695 used for gene amplification and preparation of the home-made macroarray membranes. Distribution of each gene in the 120 French isolates of this study associated with gastritis (G), duodenal ulcer (DU), gastric MALT lymphoma (MALT) or metaplasia (META). The percentages were based on the binary analysis (presence/absence/) according to the normalization process and the cutoff ratio described in Material ad Methods. "HPXXXX+", genes were designated as ubiquitous genes based on previous comparative analysis [25]; "HPXXXX" are the non-ubiquitous genes; the 48 most discriminatory genes identified as key combinations of variables (genes/axes) from the Principal Component Analysis, which were used for the clustering analysis, are in bold (Figure 2).
Click here for file
Additional file 2
CDSs of B38 strain involved in restriction/modification systems classified according to the gene status.
Click here for file
Additional file 3
Distribution of the outer membrane proteins (OMPs) encoding genes in the 7 Helicobacter pylori genome sequences. (B38, J99, 26695, HPAG1, Shi470, G27, P12). The genes are classified according to the hop, hor, hof, and hom gene families. The numbers refer to the name of the CDS in each genome (for example: 0009 in 26695 refers to HP0009, 0007 in B38 refers to HELPY0007). "x" indicates a complete absence of the gene. Two or three names separated by a "/" reveals the presence of a pseudogene.
Click here for file
Additional file 4
Number of CDSs in the B38 strain that are absent in the J99, 26695, HPAG1 or Shi470 Helicobacter pylori strains classified by protein functions.
Click here for file
Additional file 5
Number of CDSs (listed by protein functions) of the Helicobacter pylori J99, 26695, HPAG1 and Shi470, G27 and P12 strains that are absent in strain B38 respectively. * All strains: J99, 26695, HPAG1, Shi470, G27, and P12. ** The number depends on the strain chosen for reference.
Click here for file