Here are the answers to the questions:

1. What tool was used for pathway enrichment analysis?
GSEA (Gene Set Enrichment Analysis) is mentioned, but it appears that a custom method using in-house FORTRAN scripts and statistical calculations was used for pathway enrichment analysis.

2. Was a tool version number provided?
Not described for the specific pathway enrichment analysis tool, but version numbers are provided for other tools used in the analysis, such as GSNAP (version 2013-10-28) and Varscan2 (v2.3.5).

3. What gene set library was queried (eg: GO, KEGG, Reactome or other)?
Not described, but functional groups were assigned to categories such as ‘apoptosis’, ‘chemosensory response’, ‘cytoskeletal/structural’, etc.

4. Was a background gene list defined for pathway enrichment analysis?
Yes, the background gene list appears to be all coding genes (n = 14,626) and all coding genes in the reference genome (n = 18,081).

5. What statistical test was used for enrichment analysis?
Hypergeometric tests and binomial probability distributions were calculated.

6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?
Yes, the Benjamini-Hochberg False Discovery Rate (FDR) with alpha = 0.01 was used.