Figure 2.

Identification of differentially expressed genes between the rats with CIA and the control rats. (a) Number of significantly changed probe sets over time. Statistical pair-wise comparisons and empirical filtering were applied to identify differentially expressed genes (FDR <0.05, fold change >1.4, signal difference >250), as described in the Materials and methods and Results sections. Pink bars represent the number of probe sets that are significantly different from the day 0 control at the indicated time points. Blue bars represent the number of probe sets that are significantly different from the day 0 control as well as the time-matched control at the indicated time points. Red bars represent the number of probe sets that are significantly different from the day 0 control as well as the time-matched control at indicated time points, with the probe sets that fluctuated in control animals excluded. (b) Venn diagram of the differentially expressed genes. Probe sets identified as significantly changed genes at each time point were examined for overlapping over time. There are a total of 28 probe sets that significantly changed at all three time points. Note that there is a considerable amount of overlapping between day 10 and day 21; half of the genes identified at day 28 are also included in the day 10 and day 21 gene lists. CII, collagen type II; FDR, false discovery rate.