TABLE 4.

Distribution of upregulated genes in rice water stool and ileal loop samples in gene sets defined by comparative genome hybridization

SamplesUpregulated genesa
Total genesCore genesDispensable genesAbsent from California isolatesb
Stool samplec
    Patient A11910570
    Patient B10373237
    Patient C2441814915
    Two or more patientse7762112
Ileal loop sampled
    gDNA (ref.)239213208
    LB (ref.)968940
  • a Upregulated genes have log2(intensity) values >2 standard deviations above the mean of all the probed genes.

  • b Genes that were called absent in all environmental isolates but present in clinical strains. This is a subset of the dispensable gene set.

  • c Rice water stool samples collected from three cholera patients in Bangladesh (26).

  • d V. cholerae N16961 harvested from the rabbit ileal loop 8 h postinfection, using gDNA or RNA in mid-log LB culture as a reference (ref.) (41).

  • e Compilation of genes scored as upregulated in stool samples of two or more of the three patients listed in the table.