Okay, let's tackle these questions about the pathway enrichment analysis in the article. First, I need to look through the Methods section and any other relevant parts. The user wants each question answered separately, so I'll go step by step. Question 1: What tool was used for pathway enrichment analysis? Looking at the Methods section under "DMRs and DMGs Identify," it mentions that "All DMGs were subsequently analyzed with GO and KEGG pathway of the DAVID web server." So the tool here is DAVID. Question 2: Was a tool version number provided? In the same part, they mention "DAVID web server" but don't specify a version number. So the answer is no. Question 3: What gene set library was queried? They used both GO (Gene Ontology) and KEGG pathways. The answer should include both, separated by a semicolon. Question 4: Was a background gene list defined? The article doesn't mention defining a specific background gene list. It just says they analyzed DMGs with DAVID. So not described. Question 5: What statistical test was used? The DMRs were identified using Wilcoxon rank tests in MEDIPS, but for the pathway analysis, DAVID typically uses Fisher's exact test or hypergeometric test. However, the article doesn't specify the exact statistical test used in DAVID for this study. So it's not described. Question 6: Was false discovery rate correction used? Again, the article doesn't mention using FDR correction for the pathway analysis. They might have used DAVID's default methods, but it's not explicitly stated. So not described. | Question | Answer | |----------|--------| | 1. What tool was used for pathway enrichment analysis? | DAVID web server | | 2. Was a tool version number provided? | Not described | | 3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)? | GO; KEGG | | 4. Was a background gene list defined for pathway enrichment analysis? | Not described | | 5. What statistical test was used for enrichment analysis? | Not described | | 6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis? | Not described |