Okay, I'm trying to figure out how to answer these six questions about the pathway enrichment analysis from this scientific article. Let me start by reading through the provided text carefully. First, I'll check if there's a Methods section or any other part that mentions the tools used for analysis. The user mentioned focusing on the Methods but also other sections. Looking at the abstract and the rest of the content, I notice terms like "IPA pathway analysis" in the Discussion section. IPA stands for Ingenuity Pathway Analysis, which is a software tool used for functional enrichment and pathway analysis. So that answers question 1: The tool used was Ingenuity Pathway Analysis (IPA). Now, checking if there's a version number provided. I don't see any mention of specific versions in the text snippets provided, so question 2 would be "Not described." Next, for question 3, which gene set library was queried? IPA typically uses its own proprietary database, which includes pathways from various sources like GO, KEGG, Reactome, etc. But since it's a separate tool, I think the answer here is that they used Ingenuity Pathway Analysis (IPA)'s built-in gene sets. Question 4 asks if a background gene list was defined. The text doesn't mention anything about using a specific background list or the whole genome as background, so I'll have to say "Not described." For question 5, what statistical test was used? Again, the provided text doesn't specify the exact test, just that IPA was used for pathway analysis, which generally employs Fisher's exact test. But since it's not explicitly mentioned here, I should note it as "Not described." Lastly, question 6 asks if false discovery rate correction was applied. The article doesn't discuss this aspect, so again, it's "Not described." | Question | Answer | |-------------------------------------------------------------------------|---------------------------------------| | What tool was used for pathway enrichment analysis? | Ingenuity Pathway Analysis (IPA) | | Was a tool version number provided? | Not described | | What gene set library was queried (e.g., GO, KEGG, Reactome or other)? | IPA's built-in gene sets | | Was a background gene list defined for pathway enrichment analysis? | Not described | | What statistical test was used for enrichment analysis? | Not described | | Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis? | Not described | This table summarizes the information extracted from the provided text regarding pathway enrichment analysis.