Table 1.
Characteristics of the 84 H. pylori strains studied.
Table 2.
General features of the sequenced H. pylori genomes selected for microarray probe design.
Figure 1.
Comparison of HLJ005, HLJ038, and 26695 based on strain specific genes of the six sequenced genomes.
A. Comparison between HLJ005 and 26695. B. Comparison between HLJ038 and 26695. C. Comparison between HLJ038 and HLJ005. Green spots show inferred loss while orange dots show no changes in the original data. Red spots show inferred increase. Segment 1 on the X-axis: probes of 26695 strain specific genes. Segment 2: probes of G27 strain specific genes. Segment 3: probes of HPAG1 strain specific genes. Segment 4: probes of J99 strain specific genes. Segment 5: probes of P12 strain specific genes. Segment 6: probes of Shi470 strain specific genes.
Figure 2.
Comparison of HLJ005, HLJ038, and 26695 based on 0–100 kb of p12 genome.
A. Comparison between HLJ005 and 26695. B. Comparison between HLJ038 and 26695. C. Comparison between HLJ038 and HLJ005. Green spots show inferred loss while orange dots show no changes in the original data. Red spots show inferred increase. The red rectangle indicates the predicted 5.2 kb absent region both in gastric cancer strain HLJ038 and HLJ005 based on the 0–100 kb of the reference P12 chromosome.
Figure 3.
Genome comparison of eight H. pylori strains based on P12 reference sequence.
Large variable regions were labeled with colored rectangles. Predicted gastric cancer strain specific regions were labeled with a red rectangle. General genomic variation among all strains was labeled with a green rectangle. A blue rectangle represents diverse regions obtained from comparison of gastric cancer strains and superficial gastritis strains. Corresponding coding proteins were briefly labeled at the bottom of each rectangle. GC vs SG denotes comparison between the two strains of gastric cancer and the two strains of superficial gastritis. DR, different region.
Table 3.
Predicted variable genomic region based on reference genome P12.
Figure 4.
Comparison of eight H. pylori strains based on strain specific genes of six sequenced strains.
Large variable regions were labeled with colored rectangles. Predicted gastric cancer strain specific regions were labeled with a red rectangle. General genomic variations among all strains were labeled with a green rectangle. A blue rectangle represents diverse regions obtained from comparison of gastric cancer strains and superficial gastritis strains. Corresponding coding proteins were briefly labeled at the bottom of each rectangle. GC vs SG denotes comparison between the two strains of gastric cancer and the two strains of superficial gastritis.
Table 4.
Predicted variable genes based on strain specific genes of the six sequenced strains.
Figure 5.
Gene content analysis of TFS4 and TFS3 in eighty-four H. pylori isolates by PCR.
The presence of individual genes is indicated in red, and their absence in green. Non-specific amplicon is shown in black.
Table 5.
Distribution of hrgA in different diseases.