Alright, I'm trying to figure out how to answer these questions about pathway enrichment analysis based on the provided article. Let me go through each question one by one and see if I can find the relevant information. 1. **What tool was used for pathway enrichment analysis?** - Looking at the article, under sections like "Abstract" and "Discussion," they mention using co-expression network analysis but don't specify a particular tool for pathway enrichment. They talk about networks like global, tissue-preferential, and treat-response, but not the software used for pathway analysis itself. 2. **Was a tool version number provided?** - The article doesn't mention any specific versions of tools related to pathway enrichment. It's more focused on describing their database and network analyses without detailing software versions. 3. **What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** - In the "Discussion" section, they refer to GO terms, hormone responses, etc., suggesting that GO might be one of the libraries used. They also mention vindoline and vinblastine biosynthesis, which could relate to specific pathways, possibly from KEGG, but it's not explicitly stated. 4. **Was a background gene list defined for pathway enrichment analysis?** - The article doesn't describe how they set up their background gene list. It mentions constructing networks covering about 90% of C. roseus genes and identifying functional modules, but there's no explicit mention of defining a specific background list for the enrichment analysis. 5. **What statistical test was used for enrichment analysis?** - There's no information provided on the statistical tests they employed. They talk about methods like co-expression network construction and module identification but don't detail the statistics behind pathway enrichment. 6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** - Similarly, there's no mention of FDR or any multiple testing correction methods applied during the analysis. The focus seems more on network construction than the statistical handling of pathway results. Here is a summary of the information gathered based on the provided article: 1. **Tool for Pathway Enrichment Analysis:** Not described in the article. 2. **Tool Version Number:** Not provided. 3. **Gene Set Library:** Likely GO, as mentioned in discussions about gene annotations and functional modules. 4. **Background Gene List:** Not explicitly defined; however, networks covered 90% of C. roseus genes. 5. **Statistical Test Used:** Not specified in the article. 6. **False Discovery Rate Correction:** No mention of FDR or similar corrections. This information is collated based on the content provided and focuses on pathway enrichment analysis specifics as detailed in the article.