Okay, so I need to figure out how to answer these six questions about the pathway enrichment analysis in this scientific article. Let me go through each question one by one and see what information I can extract from the provided text. 1. **What tool was used for pathway enrichment analysis?** Looking at the Methods section, it says they applied Ingenuity Pathway Analysis (IPA). So the tool is IPA. 2. **Was a tool version number provided?** The text doesn't mention any specific version of IPA or Agilent's microarray. It just refers to them by name without adding version details. 3. **What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** The Methods section mentions using IPA but doesn't specify which gene set libraries were used. IPA typically uses its own proprietary databases, but since it's not explicitly stated, I can't assume. So the answer is not described. 4. **Was a background gene list defined for pathway enrichment analysis?** There's no information in the text about whether they used a specific background gene list or the entire genome as the background. It just says they used IPA without going into those details. 5. **What statistical test was used for enrichment analysis?** The Methods section doesn't specify which statistical test was employed within IPA for pathway enrichment. They mention using the Kruskal-Wallis test for gene expression changes, but that's separate from pathway analysis. 6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** Again, the article doesn't discuss any multiple testing corrections like FDR or Bonferroni. It only talks about statistical significance using P-values without mentioning how they controlled for false positives specifically in IPA. I think that's all I can gather from the text provided. | 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 | The answers are based on the information provided in the text, with "Not described" indicating that the detail wasn't mentioned or clarified.