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