<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>Gene chips or cDNA arrays of the entire set of <italic>Escherichia coli</italic> (<italic>E. coli</italic>) K12 genes were
used to measure the expression, at the mRNA level, of all 4290 protein-coding genes in
wild-type (WT) and three DNA repair-deficient derivative strains: (i) AB1157 (WT),
(ii) LR39 (<italic>ada, ogt</italic>), (iii) MV1932 (<italic>alkA1, tag-1</italic>) and (iv) GM5555 (<italic>mutS</italic>). The aim was
to investigate whether disruption of a single gene would result in significant deviation in
the expression of other genes in these organisms. We describe here a simple approach for a
stringent statistical evaluation of cDNA array data. This includes: (i) determination of
intra- and interassay variation coefficients for different expression levels, (ii) rejection of
biased duplicates, (iii) mathematical background determination, and (iv) comparison of
expression levels of identical copies of a gene. The results demonstrated a highly significant
correlation of gene expression when the mutants were individually compared with the wildtype.
Altogether, 81 deviations of the expression of 59 genes were noted, out of 12,870,
when 3-fold or greater up- or down-regulation was used as a criterion of differential
expression. In the light of current knowledge of <italic>E. coli</italic> biology, the differential expression
did not follow any logical pattern. In fact, the deviations may simply represent inter-assay
variation. The results obtained here with a simple model organism are different from those
obtained with most mammalian knockouts: disruption of the function of a single gene does
not, under good growth conditions, necessarily result in great changes in the expression of
other genes.</p>
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Comp Funct Genomics. 2002 Feb; 3(1):3-13