Skip to main content

Advertisement

Table 2 Comparison of genes significantly repressed following drug treatment with in-house curated lists of genes.

From: Genome-wide dynamics of a bacterial response to antibiotics that target the cell envelope

Entity list Genes in entity list present on microarray Vancomycin-repressed (1079 genes) Bacitracin-repressed (666 genes) Moenomycin-repressed (184 genes) Repressed by all (118 genes)
   Genes in entity list matched with repressed genes P-Value Genes in entity list matched with repressed genes P-Value Genes in entity list matched with repressed genes P-Value Genes in entity list matched with repressed genes P-Value
Amino acid metabolism 184 69 <1E-30 49 1.21E-11 9 0.033121   
ppGpp-repressed genes 189 147 <1E-30 114 <1E-16 35 <1E-09 25 <1E-10
Ribosomal protein genes 53 44 2.09E-29 27 1.57E-15 4 0.03798 3 0.0479
tRNA synthetases 28 21 5.03E-13 18 3.77E-13 3 0.028817 3 0.0088
Conservons 51 28 8.20E-12 24 1.02E-11 11 2.37E-08 10 3.87E-09
Coelichelin 12 12 5.85E-11 12 1.72E-13 2 0.032389 2 0.014
ABC transport 227 44 0.01568 48 3.85E-09 22 2.04E-08 10 0.0025
Glutamate biosynthesis 27 8 0.02838 7 0.00694 4 0.003681 3 0.0079
LAXTG sortase substrate 14 5 0.03678 5 0.00506 4 2.68E-04 4 4.77E-05
Conservon cvn 13 4 4 3.93E-04 4 5.96E-05 3 5.37E-05 3 1.41E-05
Conservon cvn 5 4 4 1.53E-07 4 5.96E-05 4 3.24E-07 4 5.37E-08
ATP synthesis 8 8 8.99E-07 7 2.72E-07     
Vitamin B12 biosynthesis 11 9 1.74E-06 7 8.86E-06     
Peptidoglycan biosynthesis (cytoplasmic) 14 10 6.31E-06 9 3.65E-07     
Gly Ser Thr biosynthesis 35 16 3.93E-04 12 2.19E-05     
Conservon cvn 10 4 4 3.93E-04 4 5.69E-05     
Conservon cvn 12 4 4 3.93E-04 4 5.69E-05     
Conservon cvn 1 4 4 0.00168 2 0.04030     
SigB regulon 87 23 0.00698 13 0.03697     
SigR regulon 26 9 0.01000 8 0.00120     
Conservon cvn 4 4 3 0.00425 2 0.04030     
Methionine biosynthesis 9 5 0.00412 3 0.03702     
Phe Tyr Trp biosynthesis 33 11 0.00280 9 0.00155     
Conservon cvn 2 3 3 2.78E-04 2 0.02138     
Val Leu Ile biosynthesis 25 11   7 0.00437     
Conservon cvn 6 4    2 0.04030 3 5.37E-05 2 0.0013
Amino acid transport 34      5 0.001202   
Carotenoid 7      2 0.01   
Desferrioxamines 4    3 0.00245   1151   
Histidine biosynthesis 26    6 0.02161     
Lysine biosynthesis 16 8 6.83E-04