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Table 3 The top 10 genes with differentially expressed levels in wild-type, tigecycline-resistant strains (109 and 200) and tigecycline-resistant mutants (109-IR and 200-IR)

From: Reduced virulence in tigecycline-resistant Klebsiella pneumoniae caused by overexpression of ompR and down-regulation of ompK35

Locus_tag

Product

Fold change

RPKM

Fold change

RPKM

109

109-IR

200

200-IR

Up-regulated genes

       

 KP1_0467

DUF1471 domain-containing protein

100.860

8.556

958.148

36.543

13.677

625.192

 KP1_0570

NAD(P)-dependent alcohol dehydrogenase

222.995

42.385

5534.362

185.672

29.898

4663.129

 KP1_1491

MBL fold metallo-hydrolase

244.571

14.271

2441.961

131.245

17.950

2404.509

 KP1_1492

RamA family antibiotic efflux transcriptional regulator

208.283

15.669

2308.962

51.519

17.314

1100.084

 KP1_1863

Lipoprotein

61.709

188.337

8823.929

37.549

92.524

3182.386

 KP1_2457

META domain-containing protein

36.716

157.346

3514.462

43.764

45.486

2194.189

 KP1_2916

Alcohol dehydrogenase AdhP

76.506

88.219

3955.111

18.991

126.001

2476.295

 KP1_3005

EamA/RhaT family transporter

25.428

4.860

127.776

49.477

3.465

261.130

 KP1_3012

NAD(P)-dependent alcohol dehydrogenase

77.347

1.918

218.789

46.273

0.680

86.970

 KP1_4241

Hypothetical protein

43.821

33.200

1481.113

56.380

16.806

1138.272

Down-regulated genes

       

 KP1_0274

Maltose ABC transporter permease MalF

− 25.282

474.168

18.524

− 6.668

25.631

4.157

 KP1_0275

Maltose/maltodextrin ABC transporter substrate-binding protein MalE

− 17.645

1277.184

73.022

− 15.171

88.873

6.814

 KP1_0276

maltose/maltodextrin ABC transporter ATP-binding protein MalK

− 35.866

1394.194

39.551

− 57.555

75.753

0.572

 KP1_0277

Maltoporin

− 40.647

1240.421

30.963

− 11.922

42.690

3.884

 KP1_0331

Murein hydrolase regulator LrgA

− 12.164

152.932

11.237

− 25.923

192.667

9.168

 KP1_0332

LrgB family protein

− 22.495

159.930

5.839

− 7.642

81.850

12.069

 KP1_1229

Nucleoside-specific channel-forming protein Tsx

− 3.768

829.324

242.142

− 65.419

1703.777

28.389

 KP1_1929

Porin OmpK35

− 17.031

193.338

10.484

− 31.287

224.113

8.822

 KP1_3535

H-type ferritin

− 5.014

240.556

45.611

− 16.395

149.821

10.912

 KP1_3976

Long-chain fatty acid transporter FadL

− 15.551

152.198

8.611

− 30.253

198.279

7.948

  1. RPKM: Read per kilobase per million