In this cohort, each antigen included was tested

for differential reactivity between patients having had PGD (n = 20) and patients without PGD (n = 19) using Student’s t-test. The baseline clinical characteristics of the two groups were well matched except that there were a higher proportion of female donors in the PGD group than in the group without PGD (see Table 1). At a significance threshold of P < 0·001 (equal to false discovery rate < 0·15), we identified only a single antigen, telomerase-associated protein 1, displaying fourfold increased reactivity in patients with PGD. Comparing changes in IgG reactivity with changes in IgM reactivity Seliciclib manufacturer for each antigen included on the microarray, however, we observed that the lower the P-values for these changes, the more frequently they changed in the same direction, see Supporting Information for Fig. S1. Requiring P < 0·05 for the differential reactivity LBH589 cost of both IgG and IgM, 16 different

proteins (corresponding to 46 different antigens, because several peptides from the same protein were usually detected), were identified. With these significance thresholds, 17 proteins were identified in all (Table 2). For each protein, the reactivity changes listed are for the most significant antigen identified. Out of the 17 proteins identified in this manner, six proteins (HSPD1, HSP90AA1, IGF1R, PRKCA, TARP, and TP53) were previously found to be differentially reactive in connection with bronchiolitis obliterans syndrome (BOS).8 Two-factor analysis of variance for these proteins, with

PGD and BOS as the factors, still identified all proteins except TP53 (P = 0·11) as displaying significant differences for PGD (P < 0·05), see Table 3 and Supporting Information for Fig. S2. We analysed the known interactions between the 17 proteins that displayed significant differential autoantibody reactivity (Table 2). This allowed us to examine whether the informative antigens formed networks with specific biological functions. Other large-scale data integrative methods have shown that well-defined interaction networks can often be functionally related Mephenoxalone to pathological processes and complex diseases.8,17 For 15 of the 17 proteins, interaction data were available, and we identified an interconnected network consisting of 12 proteins, which is significantly more than would be expected by chance (P = 3 × 10−6) as determined by randomly selecting 15 proteins out of the 260 proteins on the array where interaction data are available, recording the largest interconnected network possible to construct from these, and repeating this 107 times. Also shown in Fig. 1 are the results of hypergeometric testing on the gene ontology biological process terms assigned to the proteins in the network.