Table 1. DNA chip expression analysis.
a, List of the 23 differentially-expressed genes with lowest p-values, for rpoS-ompR against the control (Co). b, The 8 differentially-expressed genes with lowest p-values for rpoS-ompR (after 3 rounds of heat selection) compared against non heat-treated rpoS-ompR, highlighting downregulation of arginine transport and permeases.
| a | ||||||
|---|---|---|---|---|---|---|
| Rank | P-Value | FDR | FWER | +/− | Gene | Notes |
| 1 | 3E-13 | 1E-7% | 1.1E-9 | + | ompR | osmotic response regulator |
| 2 | 1.4E-9 | 3E-4% | 5.6E-6 | + | nlpD | lipoprotein |
| 3 | 3.1E-5 | 2.3% | 0.13 | + | ycjX | NTH domain |
| 4 | 3.2E-5 | 2.3% | 0.13 | + | ldhA | D-lactate dehydrogenase |
| 5 | 3.2E-5 | 2.3% | 0.13 | + | dnaK | chaperone Hsp70 |
| 6 | 3.4E-5 | 2.3% | 0.14 | − | artM | A3T permease protein |
| 7 | 5.1E-5 | 2.5% | 0.21 | + | groL | GroEL, chaperone Hsp60 |
| 8 | 5.5E-5 | 2.5% | 0.22 | + | maeB | predicted oxidoreductase |
| 9 | 5.5E-5 | 2.5% | 0.23 | + | dnaJ | chaperone with DnaK; Hsp |
| 10 | 7.1E-5 | 2.9% | 0.29 | + | ycjF | conserved inner membrane protein |
| 11 | 1.7E-4 | 6.2% | 0.67 | + | clpB | heat shock protein; Hsp |
| 12 | 1.8E-4 | 6.2% | 0.74 | + | htpG | chaperone Hsp90, Hsp C 62.5 |
| 13 | 2.2E-4 | 6.7% | 0.88 | − | artQ | A3T permease protein |
| 14 | 2.5E-4 | 7.2% | 1 | + | ogrK | prophage P2 ogr protein |
| 15 | 2.7E-4 | 7.3% | 1 | − | cspB | CspB |
| 16 | 3.1E-4 | 7.7% | 1 | + | groS | GroES, Hsp60-binding chaperone |
| 17 | 3.2E-4 | 7.7% | 1 | − | yaiA | ORF for hypothetical protein* |
| 18 | 3.6E-4 | 8.2% | 1 | + | gnty | gluconate transport associated |
| 19 | 4.0E-4 | 8.7% | 1 | + | mfd | mutation frequency decline43 |
| 20 | 4.3E-4 | 8.7% | 1 | − | cspI | cold shock-like protein |
| 21 | 4.9E-4 | 9.1% | 1 | + | hmpA | dihydropteridine reductase |
| 22 | 4.9E-4 | 9.1% | 1 | − | bcsG | gene involved in biofilm formation44 |
| 23 | 5.7E-4 | 9.8% | 1 | + | hslU | Hsp hslVU, chaperone homology |
| b | ||||||
|---|---|---|---|---|---|---|
| Rank | P-Value | FDR | FWER | +/- | Gene | Notes |
| 1 | 1.1E-07 | 0.04% | 0.0004 | − | gadW | Regulator for acid resistance |
| 2 | 2.0E-07 | 0.04% | 0.001 | − | artP | A3T component |
| 3 | 1.1E-06 | 0.1% | 0.004 | − | artQ | A3T permease protein |
| 4 | 2.2E-06 | 0.2% | 0.009 | − | artM | A3T permease protein |
| 5 | 6.2E-06 | 0.4% | 0.025 | − | yfjO | CP4-57 prophage protein* |
| 6 | 6.3E-06 | 0.4% | 0.025 | − | ybcM | DLP12 prophage; AraC type TF* |
| 7 | 7.4E-06 | 0.4% | 0.030 | − | ygiV | DNA gyrase inhibitor paralog |
| 8 | 8.0E-06 | 0.4% | 0.032 | − | yehZ | osmoprotectant (permease)45* |
Abbreviations: FDR = false discovery rate; FWER = family-wise error rate; Hsp = heat shock protein; NTH = nucleoside triphosphate hydrolase; A3T = arginine 3rd transport system
*
= hypothetical. Shock and permease proteins in yellow and pink, respectively. Up- and down-regulation are in red (+) or green (−).