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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