Okay, let me try to work through this. The user wants me to examine how the pathway enrichment analysis was conducted in the provided scientific article. They have specific questions about the methods, so I need to go through the text carefully, especially the Methods section, but also check other parts if necessary. First, I'll start by looking at the Methods section. The user mentioned that the information might be in other sections too, but the Methods should have the main details. Let me scan through the Methods again. Looking at the "RNA microarray analysis" part, here's what it says: "Expression of genes was then generated after log2 transformation and normalization with GeneSpring software (Agilent Technologies, Palo Alto CA, USA). To uncover the significance of genes for further analysis, cutoff values for gene expression results greater than ± 1.5-fold-change were further overlaid onto Ingenuity Pathway Analysis (IPA; QIAGEN, Valencia, CA, USA) to estimate canonical pathways, downstream effects, and potential upstream regulators in response to PM." Okay, so they used Ingenuity Pathway Analysis (IPA) from QIAGEN. That answers the first question: the tool is IPA. Next, the version number. The text mentions IPA but doesn't specify a version. The company is QIAGEN, but no version number is given here. So maybe the answer is "not described." For the gene set library, IPA typically uses its own proprietary content, which includes pathways from various sources like KEGG, Reactome, etc., but the user might need to know if they specified which ones. The method section doesn't mention the specific libraries used, just that they used IPA. So perhaps the answer is "not described" or maybe they just mention IPA's libraries generally. Since the question is about the gene set library queried (like GO, KEGG, etc.), but the authors didn't specify, so I should note that it's not described. Regarding the background gene list: the method says they used a cutoff of ±1.5-fold change. But does it mention a background list? The text says "overlaid onto IPA" but doesn't specify if they used the entire genome as background or another list. Since IPA usually uses its own reference, but unless the authors stated they defined a specific background, probably it's not described here. Statistical test used: The question is about what test was applied in the enrichment. IPA typically uses right-tailed Fisher's exact test for overrepresentation, but the methods don't mention the test. They might have just reported p-values without specifying, so the answer would be "not described" unless IPA's default is assumed but the user wants what's stated. False discovery rate (FDR) correction: The methods section doesn't mention FDR or multiple testing correction. They do mention in the statistical analysis part (under "Statistical analysis") that they used SPSS with p<0.05, but that's for other tests. The enrichment part doesn't specify if FDR was used. So again, "not described." Wait, but let me check other sections. The public database analysis mentions using nonparametric and t-test, but that's for the GEO analysis, not the IPA part. The main enrichment is via IPA, which the methods don't elaborate on beyond using IPA. So all the answers except the first one (tool used) are "not described." 1. **What tool was used for pathway enrichment analysis?** Ingenuity Pathway Analysis (IPA; QIAGEN). 2. **Was a tool version number provided?** Not described. 3. **What gene set library was queried (e.g., GO, KEGG, Reactome, or other)?** Not explicitly described. IPA uses proprietary libraries, but the specific gene set libraries (e.g., GO, KEGG) queried were not specified in the methods. 4. **Was a background gene list defined for pathway enrichment analysis?** Not described. The methods mention using genes with ≥±1.5-fold change as input but do not specify the background gene list used for comparison. 5. **What statistical test was used for enrichment analysis?** Not described. IPA typically uses Fisher’s exact test or other proprietary algorithms, but the specific statistical test applied was not stated. 6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** Not described. The methods do not mention FDR correction or multiple testing adjustments for enrichment analysis. --- ### Summary Table: | Question | Answer | |----------|--------| | 1. Tool used | Ingenuity Pathway Analysis (IPA) | | 2. Tool version | Not described | | 3. Gene set library | Not described (IPA’s proprietary libraries, specifics not listed) | | 4. Background gene list defined | Not described | | 5. Statistical test used | Not described | | 6. False discovery rate correction | Not described |