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Table 2 List of the 40 selected signature genes with their respective annotation and their DESeq normalized counts for each experimental condition

From: Transcriptional profiling of Klebsiella pneumoniae defines signatures for planktonic, sessile and biofilm-dispersed cells

Signature condition Locus Tag Name Annotation DESeq normalized expression (baseMeansa)  
Exponential planktonic Stationary planktonic 7 h-old biofilm 13 h-old biofilm Biofilm-dispersed K-means cluster affiliation
Exponential planktonic CH1034_160111 cydA cytochrome d terminal oxidase, polypeptide subunit I 1265.85 39855.85 25832.68 32264.31 32480.00 8
CH1034_270098 yfiD Autonomous glycyl radical cofactor 751.58 25251.54 47481.65 46582.09 42762.11 5
CH1034_230111 sodB superoxide dismutase, Fe 556.16 14965.09 16289.86 25654.59 19597.48 3
CH1034_160112 cydB cytochrome d terminal oxidase, subunit II 538.42 25053.85 12872.09 13297.53 20932.48 8
CH1034_130065   DNA polymerase 10233.37 426.38 947.64 642.98 932.75 6
CH1034_190127   Short-chain dehydrogenase/reductase SDR 2269.29 139.01 107.51 59.95 139.54 6
CH1034_280153   TonB-dependent receptor 77058.51 476.51 469.04 460.15 548.80 6
CH1034_280151   conserved protein of unknown function 3482.87 166.75 226.75 109.19 139.51 6
CH1034_280070   GntR-family bacterial regulatory protein 3552.42 331.98 281.55 332.91 258.67 6
CH1034_190125 ybiX Fe(II)-dependant oxygenase 5077.73 93.32 59.63 72.73 126.67 6
CH1034_250006 irp High-molecular-weight protein 2 260772.06 836.60 383.18 377.66 390.89 6
Stationary planktonic CH1034_130044 ygaT Carbon starvation induced protein 4.91 1192.69 3.93 8.99 5.23 10
CH1034_240015   Ferric iron ABC transporter, permease protein 30.36 8565.31 25.54 48.18 37.72 10
CH1034_130056 lpdA Dihydrolipoyl dehydrogenase 138.96 17648.19 131.68 244.32 123.71 10
CH1034_240014 fbpC Fe(3+) ions import ATP-binding protein FbpC 34.43 10241.53 38.18 56.29 33.07 10
CH1034_190101 astE succinylglutamate desuccinylase 24.92 2503.60 20.16 20.31 28.51 10
CH1034_190098 astA arginine succinyltransferase 68.46 3714.09 49.29 102.14 48.99 10
CH1034_190322 astD succinylglutamate semialdehyde dehydrogenase 10.78 788.81 10.46 20.76 19.92 10
CH1034_60005 aceK isocitrate dehydrogenase kinase/phosphatase 384.73 194088.29 347.77 342.45 696.83 10
CH1034_190201   Glycoside hydrolase 150.45 14489.44 140.46 218.27 116.28 10
CH1034_190202   Histidine kinase 253.69 17137.61 266.30 405.62 173.46 10
CH1034_220300 narY Nitrate reductase 2 subunit beta 168.04 10624.15 267.91 294.28 144.35 10
7 h-old biofilm CH1034_260051 ypfE Carboxysome structural protein 21.40 11.37 2.19 26.02 17.63 3
CH1034_220103 yncC MFS transporter 634.15 478.67 84.96 713.34 340.06 1
CH1034_180150 bssS biofilm regulator 24731.65 10960.85 1747.59 16844.60 10452.60 1
CH1034_250228 yejG hypothetical protein 11084.19 4607.89 407.32 6588.61 5798.71 1
13 h-old biofilm CH1034_220106 yidP Transcriptional regulator, GntR family protein 109.08 208.43 197.27 3617.98 125.67 3
CH1034_300308 rspB putative oxidoreductase, Zn-dependent and NAD(P)-binding 180.70 248.45 122.42 1590.79 106.96 3
CH1034_10036 ibpA heat shock chaperone 3204.61 4686.30 2252.81 29872.19 4924.76 3
CH1034_270020 bglK Beta-glucoside kinase 177.63 350.06 423.50 2757.26 316.70 3
Biofilm-dispersed CH1034_200013   conserved protein of unknown function 5547.43 8030.40 4651.95 5015.35 1035.49 10
CH1034_220241   Transcriptional regulator, LysR family 700.27 991.71 507.89 989.76 4255.17 2
CH1034_300259 truB tRNA pseudouridine synthase B 1963.34 1548.32 2797.65 1589.07 15569.23 2
CH1034_240296 yebE conserved hypothetical protein; putative inner membrane protein 385.81 448.95 315.41 608.81 5089.16 2
CH1034_190182 pspB phage-shock-protein B 147.34 256.45 198.93 298.93 1192.17 2
CH1034_190181 pspA phage-shock-protein A 855.89 991.23 730.55 1195.88 5254.86 2
CH1034_100015 cusA copper/silver efflux system, membrane component 87.92 95.96 110.78 176.25 1854.58 2
CH1034_240148   multidrug DMT transporter permease 83.27 54.21 43.60 41.28 417.64 2
CH1034_330036 envR DNA-binding transcriptional regulator 27.10 11.16 12.72 14.23 232.73 2
CH1034_130003 ytbD MFS sugar transporter 50.42 60.24 47.49 59.31 846.18 2
  1. aBaseMeans are the DESeq normalized values from the averaged triplicates of a condition