Table 2

The top scored gene gain/loss profiles

Gene identifier

NS

NWS

OR

p-value

Gene functional annotation


Penicillin (NWS-threshold: 0.58)


SAR1831(blaZ)

0.84

0.81

37.15

1.15e-06

beta-lactamase

SAR1829(blaI)

0.84

0.74

37.15

5.24e-06

transcriptional repressor

SAR1830(blaR1)

0.82

0.73

31.27

7.09e-06

beta-lactamase regulatory protein blar1

SAR0056

0.63

0.71

12.13

1.03e-05

conserved hypothetical protein

SAR0039(mecA)

0.61

0.70

10.94

1.28e-05

penicillin-binding protein pbp2a, methicillin resistance determinant mecA, transpeptidase

SAR0060(ccrA)

0.61

0.63

10.94

4.40e-05

resolvase, n-terminal domain protein

SAR0061(yycG)

0.61

0.63

10.94

4.40e-05

putative membrane protein

NWMN 0025

0.57

0.63

9.40

4.41e-05

conserved domain protein

SAR0037(ugpQ)

0.60

0.63

10.39

5.08e-05

glycerophosphoryldiester phosphodiesterase

SAR0038(maoC)

0.60

0.63

10.39

5.08e-05

dehydratase

SAR0057

0.57

0.59

9.40

9.78e-05

conserved hypothetical protein


Methicillin (NWS-threshold: 0.68)


SAR0039(mecA)

1.00

1.00

950.00

4.48e-20

penicillin-binding protein pbp2a, methicillin resistance determinant mecA, transpeptidase

SAR0037(ugpQ)

0.98

0.94

931.00

6.77e-15

glycerophosphoryldiester phosphodiesterase

SAR0038(maoC)

0.98

0.94

931.00

6.77e-15

dehydratase

SAR0056

0.95

0.85

900.00

7.55e-12

conserved hypothetical protein

SAR0036

0.64

0.80

33.78

5.77e-11

putative membrane protein

SAR0057

0.85

0.75

162.00

6.47e-10

conserved hypothetical protein

SAR0060(ccrA)

0.91

0.73

432.00

1.40e-09

resolvase, n-terminal domain protein

SAR0061(yycG)

0.91

0.73

432.00

1.40e-09

putative membrane protein

MW0028(ebpS)

0.54

0.71

22.30

2.76e-09

hmg-coa synthase


Tetracycline (NWS-threshold: 0.32)


SAAV_b3(repC)

0.54

0.64

27.69

5.70e-08

plasmid replication protein

SATW20_00660(tet)

0.54

0.64

27.69

5.70e-08

tetracycline resistance protein

SATW20_00670(pre)

0.50

0.50

24.00

3.51e-06

plasmid recombination enzyme type 3

SATW20_04620(tetM)

0.46

0.37

20.80

7.54e-05

tetracycline resistance protein tetM

SATW20_08990(virE)

0.42

0.37

19.93

7.67e-05

pathogenicity island protein

SATW20_09000

0.42

0.37

19.93

7.67e-05

pathogenicity island protein

SATW20_09010(lipA)

0.42

0.37

19.93

7.67e-05

putative protein in superantigen-encoding pathogenicity islands

SATW20_04610(thiI)

0.43

0.35

18.00

1.32e-04

putative transcriptional regulator

MW0745(int)

0.25

0.32

8.00

2.28e-04

site-specific recombinase, phage integrase family

MW0747

0.25

0.32

8.00

2.28e-04

DNA-binding helix-turn-helix protein


Erythromycin (NWS-threshold: 0.27)


SAR0050(ermA1)

0.80

0.58

76.00

1.36e-06

rRNA adenine n-6-methyltransferase

CGSSa03 12660

0.47

0.44

17.19

2.98e-05

conserved hypothetical protein

SAR0054(tnpA1)

0.75

0.39

72.00

8.12e-05

transposase for transposon

SAR1734

0.75

0.39

72.00

8.12e-05

methylase

SAR1736(spc2)

0.75

0.39

72.00

8.12e-05

spectinomycin 9-o-adenylyltransferase

SaurJH9_1711(radC)

0.72

0.38

62.00

8.83e-05

predicted protein

SAUSA300_pUSA030006

0.20

0.35

4.75

1.65e-04

replication and maintenance protein

SAR1737(tnpC2)

0.72

0.34

62.00

1.89e-04

Unknown

SAR1529

0.33

0.33

9.15

2.43e-04

conserved hypothetical protein

SATW20_04860(recF_1)

0.23

0.30

5.52

3.67e-04

recombinational DNA repair ATPase

SAR1738(tnpB2)

0.70

0.29

54.00

4.39e-04

transposase B from transposon Tn554

SauraJ_010100009720

0.23

0.27

5.52

6.60e-04

conserved domain protein


Gentamicin (NWS-threshold: 0.83)


SaurJH1_2806(aacA-aphD)

SaurJH1_2805

0.83

0.75

0.90

0.83

150.00

90.00

9.38e-11

2.95e-09

bifunctional acetyltransferase/phosphotransferase GNAT family acetyltransferase


Ciprooxacin (NWS-threshold: 0.4)


SATW20_04610(thiI)

0.35

0.45

36.00

1.33e-07

putative transcriptional regulator

SATW20_04650(cap8J)

0.32

0.40

31.57

8.25e-07

lipoprotein

SATW20_04670(capL)

0.32

0.40

31.57

8.25e-07

putative ATP/GTP-binding protein

SATW20_04780

0.32

0.40

31.57

8.25e-07

conjugation related protein

SATW20_04800

0.32

0.40

31.57

8.25e-07

replication initiation factor

SATW20_04810

0.32

0.40

31.57

8.25e-07

DNA segregation ATPase FtsK/SpoIIIE

SATW20_04830

0.32

0.40

31.57

8.25e-07

conjugative transposon protein


Summarizing information for the top scored gene gain/loss profiles. The consequent columns refer to: gene identifier of the corresponding gene family; normalized support (NS); normalized weighted support (NWS); odds ratio (OR); p-value and the gene functional annotation. Thresholds for weighted support are provided in brackets for each drug. Colored gene gain/loss profiles are provided in the supplementary the (additional file 3). Complete results for all the drugs are provided in the supplementary Excel table (additional files 2).

Wozniak et al. BMC Genomics 2012 13(Suppl 7):S23   doi:10.1186/1471-2164-13-S7-S23

Open Data