Genome-wide expression analysis by microarrays identifies two distinct transcriptomes in WKY and LEW MCs.

A. Dendogram representing the hierarchically clustering using all differentially expressed genes between WKY and LEW MCs in basal (unstimulated) and TNFα-stimulated cells. This shows that the strain (WKY or LEW) and the treatment (basal or TNFα-stimulated) effects cluster in 4 distinct groups. B. Validation of the markedly differentially expressed transcripts (fold change >10) by qRT-PCR. The upper panel shows the top differentially expressed candidates identified by microarray analysis with a false discovery rate (FDR) <0.01. The positive fold change (FC) values designate up-regulation in WKY MCs and negative FC values designate up-regulation in LEW MCs in basal conditions. The lower panel shows qRT-PCR validation for the transcripts showing differential expression in the microarray dataset. n = 4 rats, **, P<0.001. C. KEGG pathway analysis applied to differentially expressed genes between WKY and LEW MCs in basal state (WKY-LEW)basal and (WKY-LEW)TNFα identified the DNA replication and the vasculature development pathways as the most significant ones respectively. D. KEGG pathway analysis in LEW and WKY MCs treated with TNFα [(LEW)-(LEW) TNFα and (WKY)-(WKY)TNF] identified strain-specific pathways (shown in blue in the LEW and red in WKY) upon TNFα stimulation. Note that the DNA-replication pathway is the most significant one in the WKY MCs following TNFα stimulation.