Okay, let me tackle these questions one by one based on the provided article. First, the user wants to know the tool used for pathway enrichment analysis. I need to look through the Methods section and other parts of the article for clues. Looking at the Results section under the miR-SNP analysis, it mentions that statistical overrepresentation tests were done. The pathways listed include GO cellular component (like MHC protein complex and ER membrane) and Reactome (IFN-γ signaling). The table (Table 4) refers to pathways from GO and Reactome. However, the exact tool isn't named here. The Methods section might have more details. Wait, the user mentioned to check the Methods primarily. Let me recheck the Methods. The article's Methods section isn't fully provided here, but in the Results, they discuss pathway enrichment. The pathways mentioned are GO and Reactome. The工具 used isn't explicitly stated, but maybe in the context, since they used GO and Reactome, common tools like DAVID, Enrichr, or ClusterProfiler might be used. However, the article doesn't specify the tool name. Moving to the second question: tool version. Since the tool isn't mentioned, the version isn't provided either. Third, the gene set library: The pathways are from GO (Gene Ontology) and Reactome, as seen in the results and Table 4. So the libraries used are GO and Reactome. Fourth, whether a background gene list was defined. The article mentions "statistical overrepresentation tests of top miR-SNP hits" which implies comparing against a background. But specifics aren't given. The Methods might have mentioned using all genes on the array or a standard background, but since it's not in the provided text, it's not described here. Fifth, the statistical test. The term "overrepresentation tests" suggests a hypergeometric test or Fisher's exact test, which are common for enrichment. The article doesn't specify the exact test used. Sixth, FDR correction. The Results mention "statistical overrepresentation tests" and in the miR-SNP analysis, they refer to pathways with p-values. The article states "false discovery rate correction used" isn't directly mentioned, but in pathway analysis, FDR is commonly applied. However, the text doesn't explicitly say they used it. The authors mention "false discovery rate correction" in the limitations regarding miR-SNP analysis but not explicitly in the enrichment part. So, it's unclear if FDR was applied here. Putting this together, some answers can be inferred but some details are missing as the Methods section might not be fully provided here. The user should check if the full Methods section in the original article provides more details, but based on the given text, some answers are not described. 1. **What tool was used for pathway enrichment analysis?** Not explicitly described. The pathways mentioned (e.g., GO, Reactome) suggest tools like DAVID, Enrichr, or ClusterProfiler might have been used, but this is inferred, not stated. 2. **Was a tool version number provided?** No, the version number of the tool (if any) was not provided. 3. **What gene set library was queried (e.g., GO, KEGG, Reactome, or other)?** Gene sets from **Gene Ontology (GO)** and **Reactome** were used, as indicated in the results (e.g., MHC protein complex, interferon gamma signaling). 4. **Was a background gene list defined for pathway enrichment analysis?** Not described. The analysis refers to "statistical overrepresentation tests of top miR-SNP hits," but specifics about the background gene list (e.g., all genes on the array, genome-wide genes) are not provided. 5. **What statistical test was used for enrichment analysis?** The term "overrepresentation tests" implies a hypergeometric test or Fisher's exact test, but the exact test is not specified in the text. 6. **Was false discovery rate (FDR) correction used to control the number of false positives in the pathway enrichment analysis?** Not explicitly stated. While FDR correction is common in such analyses, the article does not mention its use for pathway enrichment. The authors note FDR limitations in the context of miR-SNP analysis (e.g., linkage disequilibrium), but this does not confirm FDR was applied to the enrichment results. --- ### Summary Table: | Question | Answer | |----------|--------| | 1. Tool used | Not described (likely GO/Reactome-based tools like DAVID/Enrichr, inferred) | | 2. Tool version | No | | 3. Gene set library | GO and Reactome | | 4. Background gene list defined | No | | 5. Statistical test | Not specified (implied hypergeometric/Fisher's exact) | | 6. FDR correction used | Not explicitly stated |