Here's a breakdown of the pathway enrichment analysis methods described in the provided text, answered as requested for table creation:

**1. What tool was used for pathway enrichment analysis?**

*   Not explicitly stated as a single tool. The text mentions “functional module identification” and “annotation,” implying tools were used for these purposes, but doesn't name them specifically.

**2. Was a tool version number provided?**

*   Not described.

**3. What gene set library was queried (eg: GO, KEGG, Reactome or other)?**

*   GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) are explicitly mentioned as gene set libraries used for annotation and functional module identification.

**4. Was a background gene list defined for pathway enrichment analysis?**

*   The text states they used “almost 90% of gene in *C. roseus*” for network construction which could be interpreted as the background list. However, there is no specific mention of defining a background list for the enrichment analysis itself.

**5. What statistical test was used for enrichment analysis?**

*   The text mentions “false discovery rate correction,” suggesting a statistical test was used, but does *not* specify the exact test used for the enrichment analysis.

**6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?**

*   Yes, the text specifically states that “false discovery rate correction” was used.

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Here's the data in a table format for easy collation:

| Question                                              | Answer            |
| ----------------------------------------------------- | ----------------- |
| What tool was used for pathway enrichment analysis?   | Not described     |
| Was a tool version number provided?                     | Not described     |
| What gene set library was queried?                      | GO, KEGG          |
| Was a background gene list defined?                     | Possibly, implied by use of ~90% of *C. roseus* genes |
| What statistical test was used?                         | Not described     |
| Was false discovery rate correction used?                | Yes               |