Table 3 Variations of the expression of genes involved in citrate degradation and methyl-citrate pathway.
From: Metabolic adaptation of adherent-invasive Escherichia coli to exposure to bile salts
Name | Product | Gene size | RNA-seq values (minimal medium) | RNA-seq values (bile salts) | Fold change | Fold change | p value |
|---|---|---|---|---|---|---|---|
(bp) | RPKM | RPKM | (Log2) | ||||
acnA | aconitate hydratase 1 | 2675 | 1824 | 2317 | −1.3 | −0.34 | 2.142E-01 |
acnB | aconitate hydratase 2 | 2597 | 11663 | 19016 | −1.6 | −0.70 | 2.362E-02 |
acs | acetyl-coenzyme A synthetase | 1958 | 2188 | 837 | 2.6 | 1.39 | 1.897E-04 |
citC | Citrate-lyase ligase | 1058 | 326 | 588 | 1.8 | 0.85 | 8.689E-04 |
citD | Citrate lyase acyl carrier protein | 296 | 5 | 50 | 9.1 | 3.18 | 3.731E-10 |
citE | Citrate lyase β subunit | 908 | 48 | 332 | 7.0 | 2.80 | 1.628E-17 |
citF | Citrate lyase α chain | 1532 | 55 | 362 | 6.6 | 2.72 | 8.791E-16 |
citG | dephosphocoenzyme-A | 878 | 32 | 183 | 5.6 | 2.49 | 5.951E-14 |
citT | Citrate carrier | 1463 | 271 | 732 | 2.7 | 1.43 | 2.076E-09 |
citX | Holo-citrate lyase synthase | 551 | 5 | 59 | 10.6 | 3.41 | 1.042E-13 |
ttdA | L-tartrate dehydratase subunit α | 908 | 237 | 49 | 4.8 | 2.27 | 2.511E-13 |
ttdB | L-tartrate dehydratase subunit β | 605 | 317 | 66 | 4.8 | 2.27 | 6.822E-12 |
ttdR | transcriptional activator | 932 | 635 | 341 | 1.9 | 0.90 | 5.398E-04 |
ttdT | tartrate carrier | 1463 | 724 | 312 | 2.3 | 1.21 | 1.002E-06 |
prpR | operon regulatory protein | 1586 | 192 | 435 | 2.3 | 1.19 | 1.071E-04 |
prpB | Methylisocitrate lyase | 890 | 131 | 3094 | 23.6 | 4.56 | 1.828E-37 |
prpC | 2-methylcitrate synthase | 1169 | 106 | 1313 | 12.3 | 3.62 | 3.179E-30 |
prpD | 2-methylcitrate dehydratase | 1451 | 66 | 609 | 9.3 | 3.21 | 2.654E-26 |
prpE | Propionate-CoA ligase | 1886 | 80 | 786 | 9.8 | 3.30 | 5.999E-33 |
