Here's a breakdown of the pathway enrichment analysis methods, extracted from the provided text, formatted for a table:

| **Question** | **Answer** |
|---|---|
| 1. What tool was used for pathway enrichment analysis? | Ingenuity and Webgestalt were used. |
| 2. Was a tool version number provided? | Ingenuity: Not described.  Webgestalt: Not described. |
| 3. What gene set library was queried (eg: GO, KEGG, Reactome or other)? | KEGG, Reactome, Interpro, and Molecular Signature Database (MSigDB) were queried. Additionally, authors used gene sets derived from cytogenetic mapping, and publicly available microarray results. |
| 4. Was a background gene list defined for pathway enrichment analysis? | Yes, all annotated proteins presented on the 16k protein microarray were used as background, except for cytogenetic map analyses (GSEA) where the whole human genome was used. |
| 5. What statistical test was used for enrichment analysis? | Right-tailed Fisher’s exact test was used by Ingenuity. Webgestalt used hypergeometric test. |
| 6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis? | Yes, False Discovery Rate (FDR) correction was used. |