Thinking... We need to find all explicit statements about pathway enrichment analysis. Let's search within the Methods section for "pathway enrichment analysis" or "Ingenuity Pathway Analysis (IPA)" etc. In the Methods: - In "RNA microarray analysis" paragraph: "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." This is a mention of the tool "Ingenuity Pathway Analysis (IPA)". The version is not described. Gene set libraries used: presumably from IPA's built-in libraries: canonical pathways, downstream effects, upstream regulators. But what libraries? Usually IPA uses curated databases like KEGG, GO, etc. But the article does not specify gene set libraries. Let's search. The methods may mention "Ingenuity Pathway Analysis (IPA; QIAGEN, Valencia, CA, USA)" but no version. Gene set libraries: The article says "Ingenuity Pathway Analysis (IPA; QIAGEN, Valencia, CA, USA) to estimate canonical pathways, downstream effects, and potential upstream regulators." It does not specify libraries. So "Which gene set libraries were used?" Might be not described. But maybe the authors refer to "canonical pathways" - that might refer to IPA's own library. They didn't say which gene set libraries they used (GO, KEGG, Reactome). So "Not described". Did they use a custom background? Not described. Statistical test? Might be hypergeometric? Usually IPA uses Fisher's exact test? Not sure. But the article didn't mention a specific statistical test. Let's read again the Methods part: "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." This indicates they used IPA but no statistical test described. So "Not described". Also, no mention of multiple testing correction. So "Not described". But let's confirm by reading the Results or Figures if they mention something about pathway enrichment or canonical pathways. In Results: "the top enriched pathways included the p38 MAPK signaling pathway, the ERK1/2 MAPK signaling pathway, the PI3K/AKT signaling pathway, and the NRF2-mediated oxidative stress response pathway (Fig. 1D)." But that's describing the result of enrichment analysis, not method. So not helpful. Check Supplementary Material for details. The supplementary figures might show more details. The supplementary figures are in a PDF "aging-11-102077-s001.pdf" but we cannot open because no tool. However, we can't open the supplementary PDF. The question requires only to extract what is explicitly reported. If no detail, say "Not described". Therefore: - Tool: Ingenuity Pathway Analysis (IPA). - Version: Not described. - Gene set libraries: Not described. It might be internal to IPA; they didn't mention GO, KEGG, Reactome. - Custom background: Not described. - Statistical tests: Not described. - Multiple testing correction: Not described. Thus produce a table with the six columns. But careful: The "Which gene set libraries were used?" We need to identify all gene set libraries or databases the authors queried. They did not specify any; only mention canonical pathways etc. So "Not described". Therefore produce table with columns: "Tool", "Version", "Gene set libraries", "Custom background", "Statistical tests", "Multiple testing correction". Now fill values: Tool: Ingenuity Pathway Analysis (IPA) Version: Not described Gene set libraries: Not described Custom background: Not described Statistical test(s): Not described Multiple testing correction: Not described We also need to list all tools used for enrichment analysis. Only IPA. Let's produce table. ...done thinking. | Question | Answer | |---|---| | What tool was used for pathway enrichment analysis? | Ingenuity Pathway Analysis (IPA) | | Were enrichment tool version(s) described? | Not described | | Which gene set libraries were used? | Not described | | Does the article describe using a custom or specific background gene list for enrichment analysis? | Not described | | What statistical test(s) were used in enrichment analysis? | Not described | | Was multiple testing correction / FDR applied to enrichment analysis? | Not described |