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Table 9 List of differentially expressed genesa associated with DNA repair/replication 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
DNA-repair: SOS response
EAMY_2641recN, DNA repair protein2.969.84
EAMY_3327lexA, SOS-response transcriptional repressors2.9510.27
EAMY_3296ssb, single-stranded DNA-binding protein2.229.95
EAMY_0882dinP, DNA polymerase IV2.156.96
EAMY_0805recA, recombinase A1.9711.18
EAMY_2064ruvA, Holliday junction ATP-dependent DNA helicase1.666.84
EAMY_1211uvrB, excinuclease UvrABC subunit B1.568.45
EAMY_1251dinG, ATP-dependent helicase1.237.05
EAMY_2063ruvB, Holliday junction ATP-dependent DNA helicase1.187.44
EAMY_0194uvrD, DNA helicase II1.138.55
EAMY_3297uvrA, excinuclease ATPase subunit1.019.29
DNA replication
EAMY_3296ssb, single-stranded DNA-binding protein2.229.95
EAMY_2345gyrA, DNA gyrase A subunit1.6410.46
EAMY_0725exo, 5′-3′ exonuclease1.476.31
EAMY_0844dnaQ, DNA polymerase III epsilon subunit1.366.88
EAMY_3144priB, primosomal replication protein N1.2410.24
EAMY_1122holA, DNA polymerase III delta subunit−1.216.86
  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 below 0 mean that the gene has lower expression in the (p) ppGpp0 mutant than in WT, and vice versa
  2. blog2FC valus was calculated by the log based 2 value of (p) ppGpp0 / WT at 3 h
  3. cThe average of log2CPM was calculated. CPM: count per million reads