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 |