Okay, let's tackle this query step by step. The user wants me to examine how pathway enrichment analysis was conducted in the given scientific article. They provided specific questions to answer, and I need to make sure each is addressed separately. First, I need to look through the article, particularly the Methods section. If it's not there, maybe in other sections like Results or Discussion. Let's start with question 1: What tool was used for pathway enrichment analysis? Looking through the Methods section, the authors mention using croFGD database, which integrates various tools. In the Results section, they mention GO and KEGG pathway annotations. However, the specific tool for pathway enrichment isn't explicitly stated. The Methods section might not detail the exact software. Let me check again. The abstract mentions "functional module annotation" but doesn't specify the tool. The discussion refers to integrating co-expression networks with module enrichment analysis. The references might have some clues, but the user wants the information directly from the article. Since the article doesn't explicitly state the tool used for pathway enrichment analysis, the answer would be "not described." Question 2: Tool version number. Since the tool itself isn't specified, the version number isn't provided either. Answer: Not described. Question 3: Gene set library. The article mentions GO and KEGG pathways. For example, in the Discussion, they talk about vindoline and vinblastine biosynthesis, jasmonic acid biosynthesis, hormone response, etc. The functional modules were annotated with these. So the gene set libraries are GO and KEGG. Question 4: Background gene list. The article doesn't specify whether a background gene list was defined. The methods mention constructing co-expression networks covering almost 90% of genes in C. roseus, but there's no mention of a specific background list. So answer: Not described. Question 5: Statistical test. The article mentions enrichment analysis but doesn't specify the statistical test. They refer to module enrichment analysis and PCC ranks, but the exact test (like hypergeometric, Fisher's exact) isn't stated. Answer: Not described. Question 6: FDR correction. The article doesn't mention using FDR correction. The methods talk about controlling false positives in network analysis but not specifically in pathway enrichment. Answer: Not described. I need to make sure each answer is based on the article's content. If the information isn't present, then "not described" is the correct response. The key is to avoid making up details not provided by the authors. Here is the collated information based on the article provided: | **Question** | **Answer** | |--------------|------------| | **1. What tool was used for pathway enrichment analysis?** | **Not described**. The article does not explicitly mention the specific tool used for pathway enrichment analysis. Functional module annotations and pathway enrichment are discussed, but the exact software or tool is not provided. | | **2. Was a tool version number provided?** | **Not described**. Since the tool itself is not specified, the version number is also not mentioned. | | **3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** | **GO and KEGG**. The article references annotations related to "vindoline and vinblastine biosynthesis," "jasmonic acid biosynthesis," "hormone response," and "pathogen resistance," which align with Gene Ontology (GO) and KEGG pathways. Functional modules are annotated with these libraries. | | **4. Was a background gene list defined for pathway enrichment analysis?** | **Not described**. The article does not specify whether a background gene list (e.g., all genes in *Catharanthus roseus* or a subset) was used for enrichment analysis. | | **5. What statistical test was used for enrichment analysis?** | **Not described**. The article does not detail the statistical test (e.g., hypergeometric test, Fisher’s exact test) used for pathway enrichment. It mentions "module enrichment analysis" and "PCC ranks" but does not clarify the statistical method. | | **6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** | **Not described**. The article does not state whether FDR correction or another method was applied to adjust for multiple testing in pathway enrichment analysis. | ### Notes: - The article focuses on **co-expression network analysis**, **functional module annotation**, and **network comparison** rather than explicit pathway enrichment methods. - While **GO** and **KEGG** are implied as annotation resources, the specific tools and statistical methods for pathway enrichment are not detailed in the Methods or other sections.