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## Figure 2.
Relationship of the differentially expressed genes at different phases of adjuvant
arthritis. (A) The number of differentially expressed genes (DEGs) at different phases of adjuvant
arthritis (AA) compared to the rats in the naïve (Nv) state. (B) Dendrogram visualized using TreeView software [38] representing the relationship between DEGs at different phases of AA. (C) Venn diagram showing the number of DEGs and their overlap in the three data sets:
Inc/Nv, Pk/Nv and Rec/Nv (Inc, incubation; Nv, naïve; Pk, peak; Rec, recovery). (D) Bland-Altman plots. The x-axis represents the average fold change of each sample measured by quantitative real-time
PCR (qPCR) and microarrays. The y-axis is the difference in fold change calculated by qPCR measurements minus the microarray
measurements for each sample. The solid line (y = 0.652) is the mean difference in fold change of all the samples. The two dotted
lines represent two standard deviations away from the mean difference.
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