Okay, let's tackle this query. The user wants me to look at the provided scientific article and answer six specific questions about the pathway enrichment analysis. The questions are about the tools used, version numbers, gene set libraries, background gene lists, statistical tests, and whether FDR correction was applied. First, I need to locate the Methods section where pathway analysis is described. In the given text, the Methods section isn't explicitly labeled, but there's a section discussing GO and KEGG pathway analyses. Let me scan through the text for mentions of these analyses. Looking at the "Results" and "Discussion" sections, the article mentions that GO and KEGG pathway analyses were performed. The GO analysis is referenced in the context of biological functions, and KEGG pathways are mentioned as being enriched in specific signaling pathways like PI3K-Akt. Now, for the first question: What tool was used? The article states that GO and KEGG pathway analyses were conducted. Common tools for these analyses include DAVID, GSEA, or the clusterProfiler package in R. However, the specific tool isn't named here. The text just says "GO and KEGG pathway analyses were performed," so the answer would be "not described." Second question: Was a tool version number provided? Since the tool isn't specified, the version number isn't mentioned either. So "not described." Third question: What gene set library was queried? The article mentions GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) as the libraries used. So the answer is both GO and KEGG. Fourth question: Was a background gene list defined? The article doesn't specify whether a background gene list was used. It just says co-differentially expressed DEmRNAs were analyzed. Therefore, "not described." Fifth question: What statistical test was used? The article doesn't mention the specific statistical test, like Fisher's exact test or hypergeometric test. So "not described." Sixth question: Was FDR correction used? The article doesn't state whether they applied FDR correction. The results mention significant enrichment but no details on multiple testing correction. So "not described." I need to make sure I'm not missing any implicit information. The Methods section isn't detailed here, so the answers are all "not described" except the libraries used (GO and KEGG). The user wants each answer separate, so I'll list them accordingly. Here is the collated information based on the article provided: | **Question** | **Answer** | |--------------|------------| | **1. What tool was used for pathway enrichment analysis?** | Not described. The article mentions "GO and KEGG pathway analyses were performed" but does not specify the exact tool(s) used (e.g., DAVID, GSEA, clusterProfiler, etc.). | | **2. Was a tool version number provided?** | Not described. No version number is mentioned. | | **3. What gene set library was queried?** | GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes). | | **4. Was a background gene list defined for pathway enrichment analysis?** | Not described. The article does not clarify whether a specific background gene list (e.g., all genes in the genome, genes on the microarray platform) was used. | | **5. What statistical test was used for enrichment analysis?** | Not described. The article does not specify the statistical method (e.g., hypergeometric test, Fisher’s exact test, or others). | | **6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** | Not described. The article does not mention FDR correction or other multiple testing adjustments. | ### Notes: - The article explicitly states that **GO** and **KEGG** pathway analyses were conducted but omits methodological details (tools, versions, statistical tests, and corrections). - The focus of the article is on biological interpretation rather than methodological rigor in pathway analysis.