Okay, let's tackle this query step by step. The user wants me to examine how the pathway enrichment analysis was conducted in the provided scientific article. They have six specific questions to answer, and they want each answer separate so they can compile them into a table. First, I need to locate the Methods section of the article. The user mentioned that the Methods section is the primary source, but other sections might also have relevant information. Let me start by scanning through the Methods section. Looking at the "Target genes for 3 miRNAs" part, the authors mention using 9 online databases to predict target genes. They then selected only those predicted by at least four algorithms. After that, they performed GO and pathway enrichment analyses. The exact tools used for these analyses aren't specified here. The question is asking what tool was used for pathway enrichment analysis. Since the Methods section doesn't name a specific tool, maybe it's detailed elsewhere. I should check the Results section or any supplementary materials. In the Results, under the section about the mechanisms of the miRNAs, they mention that the target genes were analyzed for GO and pathway enrichment. Still, no tool is named. The supplementary tables (3, 4, 5) list GO functional annotations and pathway analyses, but again, no tool is mentioned. The user's first question is about the tool used. Since the article doesn't specify the exact tool, the answer would be "not described." Second question: Was a tool version number provided? If the tool wasn't even named, then version number isn't applicable. Answer is "not described." Third: What gene set library was queried? The article mentions GO (Gene Ontology) and pathway analyses, but it doesn't specify if they used KEGG, Reactome, or another library. The GO part is clear, but for pathways, it's unclear. The answer might be "GO" for functional annotation and "not described" for the pathway library. Wait, the question is about the gene set library. The authors did GO functional annotation and pathway analyses. For the pathway part, they didn't specify, so that's "not described." Fourth: Was a background gene list defined? The article doesn't mention defining a background gene list. They just used the target genes predicted by four algorithms. So answer is "not described." Fifth: What statistical test was used? The article doesn't specify the statistical method. They just mention enrichment analysis but don't state if it's Fisher's exact test, hypergeometric, etc. So answer is "not described." Sixth: Was FDR correction used? The article doesn't mention any correction method for multiple testing. So answer is "not described." I need to make sure I didn't miss any details. Let me check the supplementary materials again. Supplementary Tables 3-5 have the results but no method details. The main text doesn't elaborate further. So all answers are "not described" except for the gene set library for GO, which is mentioned. Wait, the third question asks what gene set library was queried. The answer here is GO for the functional annotation part and the pathway analysis part is not specified. However, the question is about the pathway enrichment analysis. The article mentions pathway analyses but doesn't specify the database. So the answer to question 3 would be "GO" for the functional annotation and "not described" for the pathway library. But the question is phrased as a single question: "What gene set library was queried (eg: GO, KEGG, Reactome or other)?" Since they did both GO and pathway analyses, but the pathway part isn't specified, the answer would be "GO" for the functional annotation part and the pathway part is not described. However, the user is asking for the pathway enrichment analysis specifically. The question is whether the pathway enrichment used a specific library. Since the article doesn't state which one, the answer is "not described." So compiling the answers: 1. Tool: not described 2. Version: not described 3. Gene set: GO (for functional annotation), pathway library not described 4. Background: not described 5. Statistical test: not described 6. FDR: not described I need to present each answer separately as per the user's request. 1. **What tool was used for pathway enrichment analysis?** **Not described** 2. **Was a tool version number provided?** **Not described** 3. **What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** The article explicitly mentions **GO (Gene Ontology)** for functional annotation but does not specify the gene set library used for pathway enrichment analysis. 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** --- ### Summary Table | Question | Answer | |----------|--------| | 1. Tool for pathway enrichment analysis | Not described | | 2. Tool version number | Not described | | 3. Gene set library queried | GO (for functional annotation), pathway library not described | | 4. Background gene list defined | Not described | | 5. Statistical test for enrichment | Not described | | 6. FDR correction used | Not described | The authors provided limited methodological details for the pathway enrichment analysis, focusing instead on the biological interpretation of results. Key methodological parameters (e.g., tools, statistical tests, corrections) were not explicitly described in the article.