Fig. 6.
IPA comparison of proteins expressed by the NAPPA arrays and autoantigens detected in the AS cohort demonstrates a bias toward antigens involved in connective tissue and skeletal antigens. A, IPA compared the p values calculated to significant pathways assigned to all proteins expressed on the NAPPA array GST#1 with the p values calculated to significant pathways assigned to all autoantigens detected in the AS cohort only. The p value for the analysis of AS autoantigens in the connective tissue development and function pathway (p value = 4.09 × 10−11) was found to be more significant than it was in the analysis of all proteins expressed on NAPPA array GST#1 (1.54 × 10−10). B, IPA compared the p values calculated for significant pathways assigned to all proteins expressed on the NAPPA array GST#2 with the p values calculated to the significant pathways assigned to all autoantigens detected in the AS cohort only. The p values obtained from the analysis of AS autoantigens in the connective tissue disorders (p = 5.7 × 10−4) and skeletal and muscular disorders (p = 2.55 × 10−5) pathways from the NAPPA GST#2 screen were lower than they were in the analysis of all proteins expressed on NAPPA array GST#2 for those pathways, with the array p value for connective tissue disorders of 6.82 × 10−2 and skeletal and muscular disorders 1.22 × 10−2. All of the p values were calculated using a right tailed Fisher's exact test and corrected for multiple comparison with the Benjamini-Hochberg method. *, pathway significance threshold where p = 0.05.