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Table 2 The top scored gene gain/loss profiles

From: An approach to identifying drug resistance associated mutations in bacterial strains

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
  1. 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).