Here are the answers to the questions about pathway enrichment analysis:

1. What tool was used for pathway enrichment analysis?
The tools used for pathway enrichment analysis were Ingenuity, Webgestalt (Web-based Gene-set Analysis Toolkit), and GSEA (Gene Set Enrichment Analysis).

2. Was a tool version number provided?
No version number was provided for Ingenuity or Webgestalt, but the version of BRB-Array Tools used was 4.2.1, and R version was 2.10.0.

3. What gene set library was queried (eg: GO, KEGG, Reactome or other)?
The gene set libraries queried were not explicitly stated for Ingenuity, but Webgestalt and GSEA analyzed various categories, including KEGG and Reactome.

4. Was a background gene list defined for pathway enrichment analysis?
Yes, the background proteins used were all annotated proteins presented on the 16k protein microarray, except for cytogenetic map analyses (GSEA) where the whole human genome was applied.

5. What statistical test was used for enrichment analysis?
Ingenuity used right-tailed Fisher’s exact test, and Webgestalt used hypergeometric test for enrichment analyses.

6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?
Yes, False Discovery Rates (FDR) were calculated and provided in Supplementary Table 1 for differentially reactive antigens.