Table 1

Rankings of known drug resistance determining genes

Rankings before prediction

Rankings after prediction

gene id.

drug name

S

WS

OR

S

WS

OR


tet

Tetracycline

54.5

2.5

43.7

1.5

1.5

1.5

tetM

Tetracycline

14.5

11.5

7.5

4

4

4

mecA

Methicillin

1

1

1

1

1

1

mecA

Oxacillin

3

4

2

1

2

1

ermA1

Clindamycin

5.5

5.5

5.5

1

1

1

ermC

Clindamycin

907

471

907

414.5

11

191.5

ermA1

Erythromycin

3

3

4

1

1

1

ermC

Erythromycin

1527

3994.5

1006.5

413.5

28

214.5

aacA-aphD

Gentamicin

72

34

34

1

1

1

blaZ

Penicillin

163

66

223

1.5

1

2.5

mecA

Penicillin

163

8

223

11

5

52

Average ranking (excluding ermC):

53.27

15.05

60.411

2.55

1.94

7.22


Rankings of the known drug resistance determinants obtained by employing three different methods to score gene gain/loss profiles: support (S), weighted support (WS) and odds ratio (OR). Since some of the gene gain/loss profiles are assigned with the same score, we calculate their rankings as the arithmetic mean of positions of the profiles with the same score on the list sorted according to the scores; thus some of the rankings are not round numbers. The rankings were computed before and after prediction of drug resistance, which is based on the presence of the drug resistance determinants. We excluded the gene ermC from the calculations of the rankings since none of the methods were able to pull it out into the top 100 before prediction.

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

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