Okay, let's tackle this question step by step. The user wants me to look at a scientific article and answer six specific questions about the pathway enrichment analysis conducted in the study. The questions are about the tools used, versions, gene set libraries, background genes, statistical tests, and FDR correction. First, I need to recall the structure of the article. The user mentioned focusing on the Methods section but also looking elsewhere if needed. Let me start by skimming through the Methods section to find details about the pathway enrichment analysis. Looking at the Methods section, the first thing I notice is that the article discusses using the Database for Annotation, Visualization and Integrated Discovery (DAVID) for pathway enrichment analysis. That answers question 1. The tool is DAVID. Next, the version number. The Methods section doesn't mention a specific version of DAVID. So for question 2, the answer would be "not described." For question 3, the gene set library queried. In the Methods, it says they used DAVID, which typically uses KEGG, GO, and other databases. But the exact library isn't specified here. However, in the Discussion section, they mention specific pathways like "PI3K-Akt signaling pathway," "viral carcinogenesis," and "proteoglycans in cancer," which are KEGG pathways. So maybe the gene set library was KEGG. But the Methods section doesn't explicitly state it. Wait, in the Methods, under the "Pathway enrichment analysis" subsection, it says: "Pathway enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) (https://david.ncifcrf.gov/) to identify significantly enriched pathways." DAVID typically uses KEGG, GO, etc., but the article doesn't specify which databases were used. However, in the Results, they mention pathways like "viral carcinogenesis," which is a KEGG pathway. So maybe the answer is KEGG, but the article doesn't explicitly state it. Hmm. The user is asking for what the authors described. If the Methods section doesn't specify, then the answer would be "not described." But in the Discussion, they reference specific pathways. Maybe the authors used KEGG. Wait, in the Methods, the DAVID tool is used, and DAVID integrates multiple databases. The article might not specify which ones. So the answer would be "not described" unless the Methods explicitly mention it. Let me check again. The Methods section says: "Pathway enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) (https://david.ncifcrf.gov/) to identify significantly enriched pathways." No specific gene set library is mentioned here. So question 3 is "not described." Question 4: Was a background gene list defined? The Methods section doesn't mention defining a background gene list. So answer is "not described." Question 5: What statistical test was used? The Methods section doesn't specify the statistical test. DAVID typically uses Fisher's exact test or hypergeometric test. But since the article doesn't mention it, the answer is "not described." Question 6: Was FDR correction used? Again, the Methods section doesn't mention FDR correction. So answer is "not described." Putting it all together, the answers would be: 1. DAVID 2. Not described 3. Not described 4. Not described 5. Not described 6. Not described Wait, but in the Results, they mention pathways like "viral carcinogenesis," which is a KEGG pathway. However, the Methods section doesn't specify the gene set library. So unless the authors explicitly mention using KEGG, the answer remains "not described." Also, DAVID uses multiple databases, so unless they specified, we can't be sure. So the answer for question 3 is "not described." Similarly, for statistical tests, DAVID uses Fisher's exact test by default, but unless the article states it, we can't assume. So the answer is "not described." Therefore, all the answers except the first are "not described" because the Methods section doesn't provide those details. 1. **What tool was used for pathway enrichment analysis?** **DAVID** (Database for Annotation, Visualization and Integrated Discovery). 2. **Was a tool version number provided?** **Not described** (the article does not specify the version of DAVID used). 3. **What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** **Not described** (the article does not explicitly state which gene set library was queried, though pathways like "viral carcinogenesis" and "PI3K-Akt signaling pathway" are mentioned in the Results, which are KEGG pathways). 4. **Was a background gene list defined for pathway enrichment analysis?** **Not described** (no explicit mention of a background gene list in the Methods or elsewhere). 5. **What statistical test was used for enrichment analysis?** **Not described** (the article does not specify the statistical test used by DAVID for enrichment analysis). 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 mention FDR correction or any method to adjust for multiple testing). --- ### Summary Table: | Question | Answer | |----------|-----------------------| | 1 | DAVID | | 2 | Not described | | 3 | Not described | | 4 | Not described | | 5 | Not described | | 6 | Not described | The authors did not provide detailed information on the statistical methods, gene set libraries, or background gene lists used in the pathway enrichment analysis. The tool (DAVID) is explicitly mentioned, but its configuration and parameters are not described.