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Table 1 Extracted network clusters.

From: Using gene expression data and network topology to detect substantial pathways, clusters and switches during oxygen deprivation of Escherichia coli

Pyruvate processing, formate fermentation, anaerobic respiration and anaerobic synthesis of deoxyribonucleosides
1 st cluster 2 nd cluster
argininosuccinate lyase, aspartate ammonia-lyase, dimethyl sulfoxide reductase, 3,4-dihydroxy-2-butanone 4-phosphate synthase, formate hydrogenlyase complex, formate dehydrogenase pyruvate formate-lyase, fumarate reductase, FocA formate FNT transporter pyruvate formate-lyase activating enzyme, coproporphyrinogen III oxidase, anaerobic, anaerobic nucleoside-triphosphate reductase activating system, PFL-deactivase, ribonucleoside triphosphate reductase activase, lipoate synthase
Processing of hexoses
1 st cluster 2 nd cluster
1-phosphofructokinase, 6-phosphofructokinase, 6-phospho-β-glucosidase, glucokinase, mannitol-1-phosphate 5-dehydrogenase, mannose-6-phosphate isomerase, phosphoglucose isomerase, EIIMan transporter glyceraldehyde 3-phosphate dehydrogenase, 2-keto-3-deoxy-6-phosphogluconate aldolase, phosphogluconate dehydratase, phosphoglycerate kinase, triose phosphate isomerase
Iron processing
1 st cluster 2 nd cluster
2,3-dihydroxybenzoate-AMP ligase, 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase, serine activating enzyme, aryl carrier protein, enterobactin synthase multienzyme complex, isochorismatase, isochorismate synthase, enterochelin esterase cysteine desulfurase, selenocysteine lyase, thiamin (thiazole moiety) biosynthesis protein, YaaJ alanine AGSS transporter, valine-pyruvate aminotransferase
Acid response
aspartate-ammonia ligase, asparagine synthetase B, ATP phosphoribosyltransferase, CDP-diglyceride synthetase, CTP synthetase, imidazole glycerol phosphate synthase, histidinal dehydrogenase, histidinol-phosphate aminotransferase, phosphoribosyl-AMP cyclohydrolase, histidinol-phosphatase, histidinol dehydrogenase, phosphoribosyl-ATP pyrophosphatase, imidazoleglycerol-phosphate dehydratase, L-aspartate oxidase, phosphoribosylformimino-5-amino-1-phosphoribosyl-4-imidazole carboxamide isomerase, quinolinate synthase complex, protein-(glutamine-N5) methyltransferase, aspartate DAACS transporter
Nucleoside metabolism
1 st cluster 2 nd cluster
dGDP kinase, nucleoside diphosphate kinase ribonucleoside-diphosphate reductase, deoxyguanylate kinase, GTP cyclohydrolase I, guanylate kinase, guanosine-3',5'-bis(diphosphate) 3'-diphosphatase, ribonucleoside-diphosphate reductase dTDP-glucose pyrophosphorylase, dTDP kinase, UDP-glucose-hexose-1-phosphate uridylyltransferase, UDP-galactopyranose mutase, nucleoside diphosphate kinase, galactose-1-phosphate uridylyltransferase
One carbon units
gcv system, glycine dehydrogenase (decarboxylating), aminomethyltransferase glutathione synthetase, glycyl-tRNA synthetase, lipoyl-protein ligase A