Okay, let's tackle these questions about the pathway enrichment analysis in the given article. First, I need to look through the Methods section and other relevant parts to find the answers. Question 1 asks what tool was used. The article mentions "IPA pathway analysis" in the Discussion section. IPA stands for Ingenuity Pathway Analysis, which is a common tool for this kind of analysis. Question 2 is about the version number. I'll check the Methods section again. The text doesn't mention a specific version of IPA, so the answer here would be "not described." For question 3, the gene set library. The Methods section doesn't specify which library was used (like GO, KEGG, etc.), so this might be missing. The answer is probably "not described." Question 4 asks if a background gene list was defined. The Methods section doesn't mention defining a background list, so again, "not described." Question 5 is the statistical test used. The article refers to "IPA pathway analysis" but doesn't specify the exact statistical test, like Fisher's exact test or something else. So, the answer here is also "not described." Question 6 about FDR correction. The article doesn't mention using FDR or any other correction method for multiple testing, so it's "not described." I need to make sure I didn't miss any details. The Methods section is the primary place to check, but if it's not there, other sections like Results or Discussion might have hints. However, the user specified to focus on the Methods first. Since none of the details are provided in the Methods section, the answers remain as such. | Question | Answer | |----------|--------| | 1. What tool was used for pathway enrichment analysis? | **Ingenuity Pathway Analysis (IPA)** | | 2. Was a tool version number provided? | **Not described** | | 3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)? | **Not described** | | 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** | ### Notes: - The article mentions **"IPA pathway analysis"** (e.g., in the Discussion section) but does not specify the **version of IPA** used. - The **gene set library** (e.g., GO, KEGG, Reactome) or **background gene list** is not explicitly described in the Methods or other sections. - The **statistical test** (e.g., Fisher's exact test, hypergeometric test) and **FDR correction** are not detailed in the article. The results are presented as "significantly affected pathways" without methodological specifics.