Okay, let me try to work through this. The user wants me to look at the provided scientific article abstract and methods section to answer questions about pathway enrichment analysis. The questions are about the tool used, version number, gene set library, background gene list, statistical test, and FDR correction. First, I need to check the Methods section for details. Looking at the "RNA microarray analysis" part, the authors mention using Ingenuity Pathway Analysis (IPA) from QIAGEN. That answers question 1. The tool is IPA. Next, question 2 asks about the version number. The Methods section says "Ingenuity Pathway Analysis (IPA; QIAGEN, Valencia, CA, USA)" but doesn't specify a version. So the answer here is "not described." For question 3, the gene set library. IPA typically uses its own curated database, which includes various pathways and biological functions. The text doesn't mention specific libraries like GO or KEGG, so it's IPA's own database. Question 4 is about the background gene list. The Methods section mentions normalization genes were represented on the GeneChip Human Genome U133 Plus 2.0 Array. However, when it comes to pathway analysis, the background isn't explicitly stated. The cutoff for gene expression was ±1.5-fold-change, but the background gene list for enrichment isn't specified. So probably "not described." Question 5, statistical test. The Methods says they overlaid gene expression results onto IPA to estimate canonical pathways, downstream effects, and upstream regulators. IPA usually uses Fisher's exact test or similar, but the exact test isn't mentioned here. So again, "not described." Question 6, FDR correction. The Methods doesn't mention any correction method for multiple testing. So the answer is "not described." I need to make sure I didn't miss any details. The Results or other sections might have more info, but the user specified to focus on the Methods. The Supplementary Material is mentioned but not detailed here. So all the answers are based on the provided text. Let me compile them step by step. | Question | Answer | |----------|--------| | 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)? | **Ingenuity Pathway Analysis (IPA) database** (curated biological pathways and functions) | | 4. Was a background gene list defined for pathway enrichment analysis? | **Not described** (The method mentions normalization genes on the GeneChip array but does not explicitly define a background gene list for pathway analysis.) | | 5. What statistical test was used for enrichment analysis? | **Not described** (The method states results were overlaid onto IPA to estimate canonical pathways but does not specify the statistical test used.) | | 6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis? | **Not described** (No mention of FDR correction or other multiple testing adjustments.) | **Notes**: - The pathway enrichment analysis was performed using **Ingenuity Pathway Analysis (IPA)**, but no version number, specific statistical tests, or correction methods were explicitly stated. - The gene set library used by IPA is its proprietary database of curated biological pathways and functions. - The background gene list and statistical details were not provided in the Methods section.