Okay, I need to answer six specific questions about how pathway enrichment analysis was conducted in this scientific article. The focus is on the Methods section, but I can look elsewhere if needed. Let me go through each question one by one. 1. **What tool was used for pathway enrichment analysis?** Looking at the Methods section, under RNA microarray analysis, it mentions that they used Ingenuity Pathway Analysis (IPA) from QIAGEN. So the tool is IPA. 2. **Was a tool version number provided?** I don't see any mention of specific version numbers for IPA in the Methods or elsewhere. It just says "Ingenuity Pathway Analysis (IPA; QIAGEN, Valencia, CA, USA)" without a version. 3. **What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** The article doesn't specify which gene sets were used within IPA. It just mentions they used IPA for canonical pathways and upstream regulators, so it's likely using IPA's own libraries but not explicitly stated. 4. **Was a background gene list defined for pathway enrichment analysis?** There’s no information provided about a background gene list. They normalized the data and set a fold-change cutoff of ±1.5, but it doesn’t mention anything about a background list beyond that. 5. **What statistical test was used for enrichment analysis?** The Methods section talks about using nonparametric and t-test analysis for differentially expressed genes in the GEO database but doesn't specify what IPA uses for pathway enrichment. IPA typically uses Fisher's exact test, but since it's not mentioned here, I can only note that the test isn’t described. 6. **Was false discovery rate correction used to control the number of false positives?** The article doesn't mention FDR correction in relation to pathway analysis. It does talk about statistical significance with P < 0.05 but not specifically for multiple testing corrections in IPA. | Question | Answer | |----------|--------| | **1. What tool was used for pathway enrichment analysis?** | Ingenuity Pathway Analysis (IPA) from QIAGEN. | | **2. Was a tool version number provided?** | No, the version number is not specified. | | **3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** | Not explicitly stated; likely IPA's own libraries. | | **4. Was a background gene list defined for pathway enrichment analysis?** | Not described in the article. | | **5. What statistical test was used for enrichment analysis?** | Not described; possibly Fisher's exact test as per IPA's typical use, but not confirmed. | | **6. Was false discovery rate correction used to control the number of false positives?** | No information provided on FDR correction. | This table summarizes the findings based on the available details in the article.