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Table 3 Selected DEGs in LYSZa6 compared to LYSZa5 related to alginate biosynthesis and type VI secretion system

From: Pseudomonas aeruginosa modulates alginate biosynthesis and type VI secretion system in two critically ill COVID-19 patients

Gene

Product name

Base mean

Fold change

Adj

p-value

LYSZa2 Mean

LYSZa3 Mean

algD

GDP-mannose 6-dehydrogenase AlgD

2956.90

138.79

2.47E–170

39.33

6375.00

algX

Alginate biosynthesis protein AlgX

271.80

45.97

1.05E–75

10.67

585.67

algL

Poly(beta-d-mannuronate) lyase precursor AlgL

283.61

44.85

1.98E–74

11.33

609.00

algJ

Alginate o-acetyltransferase AlgJ

118.03

32.97

3.93E–33

6.33

248.67

algE

Alginate production outer membrane protein AlgE precursor

254.48

25.19

1.11E–61

18.33

535.33

algA

Phosphomannose isomerase/guanosine 5'-diphospho-d-mannose pyrophosphorylase

481.88

21.52

9.22E–64

39.00

1000.67

algF

Alginate o-acetyltransferase AlgF

152.00

18.68

7.50E–42

14.33

314.67

alg8

Alginate biosynthesis protein Alg8

292.51

14.91

1.09E–59

34.67

599.33

alg44

Alginate biosynthesis protein Alg44

195.56

14.43

3.38E–61

23.67

403.00

algK

Alginate biosynthetic protein AlgK precursor

135.65

10.35

6.37E–39

21.67

272.67

algI

Alginate o-acetyltransferase AlgI

218.14

8.40

7.47E–47

43.00

427.33

algG

Alginate-c5-mannuronan-epimerase AlgG

356.62

4.45

4.15E–53

121.33

644.33

clpV1

ClpV1

5315.67

− 4.08

7.48E–33

7854.33

2309.33

PA3904

PAAR4

1457.06

− 4.17

3.79E–33

2178.00

631.67

PA2702

Tse2

280.90

− 4.35

2.50E–29

419.33

117.33

PA2774

Tse4

296.61

− 4.37

4.85E–26

461.67

122.33

PA2775

Tsi4

133.81

− 4.71

7.24E–19

212.67

52.33

vgrG1

VgrG1

2637.35

− 4.74

1.56E–50

3969.33

1016.67

PA0093

Tse6

947.79

− 4.91

3.88E-–46

1469.00

360.00

PA3905

Type VI effector chaperone for Tox-Rease, TecT

1073.56

− 4.95

1.10E–53

1671.00

403.00

PA0082

TssA1

1449.46

− 5.32

1.76E–55

2265.00

515.00

PA2703

Tsi2

98.26

− 5.56

5.99E–24

156.67

33.00

PA0094

EagT6

251.06

− 5.79

1.43E–38

401.67

82.00

PA3484

Tse3

544.56

− 5.86

1.50E–54

869.33

174.33

stk1

Stk1

263.85

− 5.90

1.38E–56

423.00

84.67

PA5266

VgrG6

396.48

− 6.81

6.50E–47

654.33

113.33

PA1667

HsiJ2

678.54

− 6.99

2.41E–100

1119.67

188.67

PA1656

HsiA2

3257.03

− 7.01

4.84E–80

5349.67

911.33

PA1662

clpV2

2538.08

− 8.98

3.88E–108

4332.33

564.33

PA1661

HsiH2

693.51

− 9.91

1.55E–110

1186.67

142.00

PA1666

Lip2

340.97

− 10.48

2.48E–72

589.00

65.67

stp1

Stp1

327.95

− 10.61

1.67E–70

562.67

62.67

hcpA

Secreted protein Hcp

72.34

− 10.75

7.25E–26

125.33

13.67

PA1665

Fha2

840.73

− 10.96

1.12E–108

1456.67

155.33

PA1660

HsiG2

907.03

− 11.05

1.78E–125

1551.67

167.33

PA1669

IcmF2

2052.74

− 11.08

6.20E–107

3547.33

375.67

hcpB

Secreted protein Hcp

204.27

− 11.30

8.81E–47

358.00

36.67

PA1668

DotU2

487.58

− 11.30

1.39E–105

836.33

88.00

PA1663

Sfa2

883.17

− 12.92

4.47E–74

1556.67

139.33

PA3334

Acp3

236.04

− 13.79

1.82E–73

415.67

35.33

PA1657

HsiB2

2539.11

− 14.39

1.32E–112

4445.00

366.00

PA1659

HsiF2

480.65

− 17.06

4.25E–89

843.33

59.00

PA1658

HsiC2

5746.91

− 17.11

4.82E–66

10,179.00

695.67

  1. Filtering criteria are fold change  4, adjusted p-value < 0.05 and base mean 20. Full list of DEGs is included in Additional file 9: Table S7