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. 2015 Feb 11;59(3):1707–1717. doi: 10.1128/AAC.04581-14

TABLE 2.

Differentially expressed ORFs organized by functional category

ORF category by function(s) No. (%) of ORFs with change in expression fora:
2-h treatment vs no treatment
24-h treatment vs no treatment
24-h vs 2-h treatment
Upregulated Downregulated Upregulated Downregulated Upregulated Downregulated
Cellular processes and signaling
    Cell cycle control, cell division, and chromosome partitioning 1 (0.2) 5 (1.9) 2 (0.9) 1 (0.3)
    Cell wall, membrane, and envelope biogenesis 14 (3.5) 17 (6.6) 1 (8.3) 18 (8.3) 10 (3.2)
    Cell motility 3 (0.7) 1 (0.4) 1 (8.3) 1 (0.5) 3 (1.0)
    Posttranslational modification, protein turnover, and chaperones 20 (5.0) 10 (3.9) 10 (4.6) 14 (4.5)
    Signal transduction mechanisms 18 (4.5) 8 (3.1) 3 (25) 2 (0.9) 16 (5.2)
    Intracellular trafficking, secretion, and vesicular transport 4 (1.0) 4 (1.6) 1 (8.3) 3 (1.4) 3 (1.0)
    Defense mechanisms 4 (1.0) 4 (1.6) 3 (1.0)
Information storage and processing
    Translation, ribosomal structure, and biogenesis 3 (0.7) 36 (14.0) 29 (13.4) 3 (1.0)
    Transcription 41 (10.0) 11 (2.7) 2 (7.1) 1 (8.3) 9 (4.1) 33 (10.7)
    Replication, recombination, and repair 9 (2.2) 9 (3.5) 5 (2.3) 3 (1.0)
Metabolism
    Energy production and conversion 47 (11.7) 28 (10.9) 6 (21.4) 29 (13.4) 41 (13.3)
    Amino acid transport and metabolism 65 (16.2) 21 (8.2) 5 (17.9) 2 (16.7) 25 (11.5) 43 (14.0)
    Nucleotide transport and metabolism 8 (2.0) 18 (7.0) 17 (7.8) 7 (2.3)
    Carbohydrate transport and metabolism 55 (13.7) 36 (14.0) 3 (10.7) 34 (15.7) 40 (13.0)
    Coenzyme transport and metabolism 7 (1.7) 13 (5.1) 1 (3.6) 8 (3.7) 7 (2.3)
    Lipid transport and metabolism 24 (6.0) 6 (2.3) 4 (14.3) 1 (8.3) 3 (1.4) 17 (5.5)
    Inorganic ion transport and metabolism 20 (5.0) 18 (7.0) 3 (10.7) 1 (8.3) 20 (9.2) 20 (6.5)
    Secondary metabolite biosynthesis, transport, and catabolism 25 (6.2) 2 (0.8) 5 (17.9) 1 (8.3) 2 (0.9) 17 (5.5)
Poorly characterized
    General function prediction only 19 (4.7) 3 (1.2) 1 (3.6) 2 (0.9) 11 (3.6)
    Function unknown 65 (16.2) 26 (10.1) 6 (21.4) 3 (25) 21 (9.7) 57 (18.5)
a

Percentages total more than 100% due to ORFs belonging to multiple functional categories.