Okay, let's tackle this question step by step. The user wants me to look at the provided scientific article and answer six specific questions about the pathway enrichment analysis conducted. The focus is on the Methods section, but other sections might also hold relevant information. First, I need to carefully read through the Methods section and any other parts mentioned in the question. Let me start by scanning the Methods section for details on pathway enrichment analysis. In the "DEG enrichment analysis" subsection, the authors mention using Blast2GO for Gene Ontology (GO) enrichment analysis. They also mention using KOBAS software to obtain DEG-related KEGG pathways. So for question 1, the tools used are Blast2GO and KOBAS. Next, question 2 asks if a tool version number was provided. Looking at the text, when they mention KOBAS, they don't specify a version. Similarly, Blast2GO is mentioned without a version. So the answer here is no for both tools. For question 3, they used GO and KEGG as the gene set libraries. The text says "Gene Ontology (GO) enrichment analysis" and "KEGG pathways". So the answer is GO and KEGG. Question 4 asks if a background gene list was defined. The article doesn't explicitly mention defining a background gene list. They just talk about using the assembled transcriptome and DEGs. So it's possible that the background was the entire transcriptome, but the authors didn't explicitly state this. Therefore, the answer is "not described". Question 5 is about the statistical test used. The authors mention that pathways with a p-value less than 0.05 were considered significant. However, they don't specify the exact statistical test (like Fisher's exact test or hypergeometric test). So the answer here is "not described". Question 6 asks if FDR correction was used. The text says that for DEG analysis, they adjusted p-values using Benjamini and Hochberg’s approach to control FDR. However, for the enrichment analysis, they only mention that p-values were considered significant if less than 0.05, but don't specify if FDR correction was applied here. Therefore, the answer is "not described". I need to make sure I didn't miss any details. Let me check the other sections again. The Abstract and Results don't mention the tools or methods for enrichment beyond what's in the Methods. The Additional files might have more, but the user hasn't provided those. So sticking to the Methods section, my answers should be accurate. Here is the collated information regarding the pathway enrichment analysis from the article: | **Question** | **Answer** | |--------------|------------| | **1. What tool was used for pathway enrichment analysis?** | **Blast2GO** (for GO enrichment) and **KOBAS** (for KEGG pathway analysis). | | **2. Was a tool version number provided?** | **No**. The article does not specify version numbers for either Blast2GO or KOBAS. | | **3. What gene set library was queried?** | **GO** (Gene Ontology) and **KEGG** (Kyoto Encyclopedia of Genes and Genomes). | | **4. Was a background gene list defined?** | **Not described**. The article does not explicitly state whether a background gene list was defined for the enrichment analysis. | | **5. What statistical test was used for enrichment analysis?** | **Not described**. The article mentions using *p*-values (threshold <0.05) but does not specify the exact statistical test (e.g., Fisher’s exact test, hypergeometric test). | | **6. Was false discovery rate correction used?** | **Not described**. While the article mentions adjusting *p*-values for differential gene expression using Benjamini–Hochberg’s approach, it does not clarify whether this correction was applied to the pathway enrichment analysis. | --- **Notes**: - The enrichment analysis tools (Blast2GO and KOBAS) are explicitly mentioned in the **Methods** section. - The absence of version numbers, background gene list details, statistical test specifics, and FDR correction for enrichment analysis is confirmed based on the provided text.