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Figure 3 | BMC Genomics

Figure 3

From: Comparative tissue transcriptomics reveal prompt inter-organ communication in response to local bacterial kidney infection

Figure 3

Commonly upregulated genes during early local inflammation. A. Hierarchical clustering of differentially expressed genes (rows) from studies a-d (columns) (Table 2). Yellow represents differentially expressed genes, while blue are non-differentially expressed. Genes differentially expressed in all datasets are shown in text. B and C. Genes in each study were ranked after adjusted P-value (B) or Bayes statistic (C), the rank number was plotted against adjusted P- value (B) and Bayes statistic (C). Study a - green, b - blue, c - red, and d - black. The dashed horizontal line shows an adjusted P- value of 0.5 (B) or a Bayes statistic of -2.5 (C). D. Gene names in all four studies were replaced with random names. Amounts of differentially expressed genes present in all four studies were plotted against Bayes statistic threshold. Error bars show SD of 20 randomized trials. E. Venn diagram showing the relationship between probes differentially expressed (Bayes statistc ≥-2.5) at 8 h (orange) and 5 h (green), respectively. The purple circle represents probes differentially expressed 8 h post-infection with adjusted P-value <0.05 and fold expression >2. Amounts of probes are given. F. Relative expression levels of core genes quantified by qRT-PCR. Expression levels in UPEC- (white bars) and PBS -injected tissue were normalized to that of PBS injected-tissue. *indicate a P-value <0.05 defined by Student's t-test between PBS and UPEC injected samples, # indicate a P-value <0.10. Error bars show SD, n = 3.

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