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We classified the 479 genes into major functional classes (Fig. 2a), as detailed in section 3 in Supplementary information S1 (notes).
Proteome analyses revealed that rhodomyrtone at subinhibitory concentration (0.174 µg/ml) affected the expression of several major functional classes of whole cell proteins in MRSA.
Oxidative stress-responsive and detoxification genes represented the major functional classes that responded to chloroquine, with 11 genes being down-regulated and 2 being up-regulated (Table 1).
Cell wall and cell wall processes, and intermediary metabolism and respiration were the two major functional classes of proteins represented in the infected lung.
Genes in major functional classes were examined for their correlations with the principal eigen-genes and eigen-proteins shown in Figure 4A.
The major functional classes of regulated genes in Chl 50Pb were oxidative stress, immunity, protein synthetic machinery, transport (see Supplementary Information Text S1), and other genes of unknown function (Fig. 2).
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As in other Actinobacteria [ 48– 50], the major functional class identified are substrate binding proteins of ABC transport systems.
This class of proteins constitutes a major functional class that is regulated by bacterial sRNAs in E.coli and Salmonella (Waters and Storz, 2009).
As anticipated, the major functional class represented among the up-regulated genes were transcriptional activators (25%) which included two members of the well characterised CBF gene family.
The final major functional class contained 26 assembled sequences assigned to have transporter or carrier activities; twelve sequences were annotated as ion transporters.
As shown in Figure 4, "Phages, prophages, transposable elements, and plasmids" was the major functional class structuring the genomes in every niche dimension.
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