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Table 2 List of differentially expressed genesa associated with virulence for WT at 6 h versus WT at 3 h

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

AccessionGene descriptionLog2FCbMeanc
T3SS
EAMY_0519hrpK, pathogenicity locus protein1.386.50
EAMY_0520hsvA, Hrp-associated systemic virulence protein1.64.98
EAMY_0521hsvB, Hrp-associated systemic virulence protein1.44.58
EAMY_0522hsvC, Hrp-associated systemic virulence protein1.025.64
EAMY_0525hrcU, type III secretion protein1.686.64
EAMY_0526hrcT, type III secretion apparatus protein1.715.51
EAMY_0527hrcS, type III secretion protein1.94.54
EAMY_0528hrcR, type III secretion apparatus protein1.756.51
EAMY_0529hrcQ, type III secretion system apparatus protein1.757.37
EAMY_0530hrpP, type III secretion protein1.836.74
EAMY_0531hrpO, type III secretion protein1.786.58
EAMY_0532hrcN, type III secretion system ATPase1.727.64
EAMY_0533hrpQ, type III secretion system protein1.677.37
EAMY_0534hrcV, type III secretion inner-membrane protein1.68.13
EAMY_0535hrpJ, type III secretion system protein1.637.86
EAMY_0536hrpL, RNA polymerase sigma factor1.047.89
EAMY_0542hrpA, Hrp pili protein2.5411.62
EAMY_0543hrpB, type III secretion system protein1.679.49
EAMY_0544hrcJ, type III secretion inner-membrane protein1.78.47
EAMY_0545hrpD, type III secretion protein1.696.78
EAMY_0546hrpE, type III secretion apparatus protein1.656.19
EAMY_0547hrpF, type III secretion protein1.717.77
EAMY_0548hrpG, type III secretion protein1.718.30
EAMY_0549hrcC, type III secretion system outer membrane porein1.689.38
EAMY_0550hrpT, type III secretion lipoprotein1.716.39
EAMY_0551hrpV, type III secretion protein1.826.37
EAMY_0552hrpN, harpin protein2.1110.21
EAMY_0553orfA, Tir chaperone family protein1.618.27
EAMY_0554orfB, avirulence protein1.648.76
EAMY_0555orfC, HrpW-specific chaperone1.757.15
EAMY_0556hrpW, harpin protein1.689.40
EAMY_0557dspE, Hrp secreted pathogenicity-like protein1.8611.32
EAMY_0558dspF, Hrp secreted pathogenicity-like protein2.118.21
EAMY_0653eop2, type III effector1.368.74
  1. aDifferentially expressed genes (DEGs) between the WT at 6 h and at 3 h with |log2FC| value ≥ 1 and an adjusted p value < 0.05. FC: fold change. WT: wild type. FC values over 0 mean that the gene has higher expression in WT at 6 h than at 3 h
  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