Here are the answers to the questions:

1. What tool was used for pathway enrichment analysis?
The article does not explicitly mention a specific tool used for pathway enrichment analysis, but it mentions "module enrichment analysis" and "network analysis strategy", suggesting that a custom or proprietary method may have been used. However, one of the figures is mentioned to be generated using ATTED-II, which is a database of co-expressed genes, but not typically considered a pathway enrichment tool.

2. Was a tool version number provided?
Not described.

3. What gene set library was queried (eg: GO, KEGG, Reactome or other)?
The article mentions that the annotation of functional modules covered "vindoline and vinblastine biosynthesis, jasmonic acid biosynthesis, hormone response and pathogen resistance", but does not specify which gene set library was used. However, it is mentioned that GO terms are integrated into the database.

4. Was a background gene list defined for pathway enrichment analysis?
Not described.

5. What statistical test was used for enrichment analysis?
Not described.

6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?
Not described.