Table 2 Variations of the expression of genes involved in glycolysis, TCA cycle and formation of acetyl-coA.
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) | ||||
aceE | Pyruvate dehydrogenase E1 | 2663 | 6420 | 11797 | −1.8 | −0.88 | 1.188E-02 |
aceF | Dihydrolipoyllysine-residue acetyltransferase | 1892 | 2620 | 3886 | −1.5 | −0.57 | 6.618E-02 |
ackA | acetate kinase | 1202 | 2740 | 4056 | −1.5 | −0.57 | 7.020E-02 |
acs | acetyl-coenzyme A synthetase | 1958 | 2188 | 837 | 2.6 | 1.39 | 1.897E-04 |
eno | Enolase | 1298 | 9777 | 15019 | −1.5 | −0.62 | 6.921E-02 |
fbaA | Fructose-bisphosphate aldolase class 2 | 1079 | 3314 | 3828 | −1.2 | −0.21 | 4.847E-01 |
fbaB | Fructose-bisphosphate aldolase class 1 | 1124 | 943 | 837 | 1.1 | 0.17 | 4.857E-01 |
fbp | Fructose-1.6-bisphosphatase | 998 | 3314 | 5750 | −1.7 | −0.79 | 1.384E-02 |
fumA | Fumarate hydratase class I. aerobic | 1646 | 7038 | 9348 | −1.3 | −0.41 | 1.869E-01 |
fumB | Fumarate hydratase class I. anaerobic | 1646 | 771 | 415 | 1.9 | 0.90 | 5.607E-05 |
fumC | Fumarate hydratase class II | 1403 | 1122 | 884 | 1.3 | 0.34 | 1.468E-01 |
gapA | glyceraldehyde-3-phosphate dehydrogenase A | 995 | 25736 | 36899 | −1.4 | −0.52 | 1.405E-01 |
glk | glucokinase | 965 | 832 | 912 | −1.1 | −0.13 | 6.037E-01 |
gltA | Citrate synthase | 1283 | 7479 | 15175 | −2.0 | −1.02 | 7.423E-04 |
gpmA | bisphosphoglycerate-dependent phosphoglycerate | 752 | 10216 | 19188 | −1.9 | −0.91 | 4.772E-03 |
gpmM | bisphosphoglycerate-independent phosphoglycerate | 1544 | 1282 | 1810 | −1.4 | −0.50 | 7.967E-02 |
icd | Isocitrate dehydrogenase [NadP] | 1250 | 17987 | 30473 | −1.7 | −0.76 | 1.944E-02 |
lpd | Dihydrolipoyl dehydrogenase | 1424 | 10039 | 20656 | −2.1 | −1.04 | 1.135E-03 |
mdh | Malate dehydrogenase | 938 | 5402 | 8506 | −1.6 | −0.66 | 2.854E-02 |
pfkA | 6-phosphofructokinase isozyme 1 | 962 | 1283 | 4244 | −3.3 | −1.72 | 1.369E-11 |
pgi | glucose-6-phosphate isomerase | 1649 | 4480 | 5251 | −1.2 | −0.23 | 4.652E-01 |
pgk | Phosphoglycerate kinase | 1163 | 2762 | 4408 | −1.6 | −0.67 | 3.299E-02 |
pta | Phosphate acetyltransferase | 2144 | 1355 | 1764 | −1.3 | −0.38 | 1.523E-01 |
pykA | Pyruvate kinase II | 1442 | 1163 | 1360 | −1.2 | −0.23 | 3.798E-01 |
pykF | Pyruvate kinase I | 1412 | 2019 | 5004 | −2.5 | −1.31 | 7.772E-07 |
sdhA | Succinate dehydrogenase flavoprotein subunit | 1766 | 8036 | 14377 | −1.8 | −0.84 | 1.123E-02 |
sdhB | Succinate dehydrogenase iron-sulfur subunit | 716 | 4221 | 6984 | −1.7 | −0.73 | 2.521E-02 |
sdhC | Succinate dehydrogenase cytochrome b556 subunit | 389 | 4494 | 8916 | −2.0 | −0.99 | 1.946E-03 |
sdhD | Succinate dehydrogenase hydrophobic membrane | 347 | 2126 | 3986 | −1.9 | −0.91 | 6.527E-04 |
sucA | 2-oxoglutarate dehydrogenase E1 component | 2801 | 18453 | 38038 | −2.1 | −1.04 | 1.922E-03 |
sucB | Dihydrolipoyllysine-residue succinyltransferase | 1217 | 9625 | 19122 | −2.0 | −0.99 | 5.780E-03 |
sucC | Succinyl-CoA synthetase beta chain | 1168 | 7109 | 12688 | −1.8 | −0.84 | 1.840E-02 |
sucD | Succinyl-CoA ligase [adP-forming] subunit α | 869 | 9683 | 12034 | −1.2 | −0.31 | 3.924E-01 |
tpiA | Triosephosphate isomerase | 767 | 4649 | 4399 | 1.1 | 0.08 | 8.098E-01 |
