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Table 8 List of differentially expressed genesa associated with nucleitide metabolism for the (p) ppGpp0 mutant versus WT at 3 h

From: The stringent response regulator (p) ppGpp mediates virulence gene expression and survival in Erwinia amylovora

AccessionGene DescriptionLog2FCMeanb
Purine
 GMP
  EAMY_2568guaB, inosine-5′-monophosphate dehydrogenase2.9410.85
  EAMY_2567guaA, GMP synthase1.669.06
  EAMY_2859guaC, GMP reductase1.558.44
 IMP
  EAMY_2052purT, phosphoribosylglycinamide formyltransferase II1.799.79
  EAMY_2542purM, phosphoribosylformylglycinamidine cyclo-ligase1.7410.49
  EAMY_2610purl, FGAM synthase1.510.89
  EAMY_2529purC, SAICAR synthase1.49.8
  EAMY_0262purH, bifunctional purine biosynthesis protein1.289.07
  EAMY_1965purU, formyltetrahydrofolate deformylase1.168.47
  EAMY_2543purN, phosphoribosylglycinamide formyltransferase1.028.57
  EAMY_0261purD, phosphoribosylamine-glycine ligase19.04
  EAMY_2978deoD, uridine phosphorylase2.349.11
  EAMY_0884gpt, xanthine phosphoribosyltransferase1.897.3
  EAMY_0864pucG, serine-pyruvate aminotransferase1.595.14
Pyrimidine
 UMP
  EAMY_1900pyrF, orotidine-5′-phosphate decarboxylase2.167.42
  EAMY_2932carA, carbamoyl-phosphate synthase small subunit1.9311.18
  EAMY_2283cdd, cytidine deaminase1.886.95
  EAMY_0366pyrB, aspartate carbamoyltransferase1.838.42
  EAMY_2931carB, carbamoyl-phosphate synthase large chain1.2511.53
  EAMY_0074dut, deoxyuridine 5′-triphosphate nucleotidohydrolase1.537.54
  EAMY_0210udp, uridine phosphorylase1.477.34
  EAMY_0365pyrI, aspartate carbamoyltransferase1.277.49
  EAMY_2257udk, uridine kinase1.047.62
 CMP
  EAMY_0737pyrG, CTP synthase2.1210.37
  EAMY_1346cmK, cytidylate kinase1.067.98
 TMP
  EAMY_2980deoA, thymidine phosphorylase1.637.04
  1. aDifferentially expressed genes (DEGs) between the (p) ppGpp0 mutant and WT at 3 h with |log2FC| value ≥ 1 and an adjusted p value < 0.05. WT: wild type. FC: fold change. FC values over 0 mean that the gene has higher expression in the (p) ppGpp0 mutant than in 1valus was calculated by the log based 2 value of (p) ppGpp0 / WT at 3 h
  2. cThe average of log2CPM was calculated. CPM: count per million reads