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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

      
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BMC Genomics

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