Okay, let's tackle this query. The user wants me to determine how the pathway enrichment analysis was conducted in the provided scientific article. They need answers to six specific questions about the methods used. First, I need to locate the Methods section. The article's Methods section is where such details are typically found. However, the user mentioned that information might also be in other sections, so I should check the Results or even the Abstract if necessary. Looking through the provided text, the Methods section isn't included, but the Results and Discussion sections mention some details. For example, in the miR-SNP analysis part, the authors refer to "statistical overrepresentation tests of top miR-SNP hits yielded two receptor-mediated signaling pathways." They also mention specific pathways like the histamine H1 receptor pathway and the 5-HT2 type receptor mediated signaling pathway, and they reference databases like GO and Reactome. The user's first question is about the tool used. The article mentions "statistical overrepresentation tests," which is a common term in pathway analysis. But the specific tool isn't named here. The authors might have used a standard tool like DAVID, GSEA, or another, but it's not specified. So the answer would be "not described." Next, the version number. Since the tool isn't named, the version is also unknown. Answer: not described. For the gene set library, the article mentions GO (MHC protein complex, integral component of the luminal side of endoplasmic reticulum membrane) and Reactome (interferon gamma signaling pathway). So the libraries are GO and Reactome. Background gene list: The article doesn't explicitly state how the background was defined. The question is whether they used all genes, a custom list, etc. Since it's not mentioned, the answer is not described. Statistical test: The authors mention "statistical overrepresentation tests," which could imply a hypergeometric test or Fisher's exact test, which are commonly used in overrepresentation analysis. However, the exact test isn't specified, so answer is not described. False discovery rate (FDR) correction: In the miR-SNP analysis, they mention "statistical overrepresentation tests," but the correction method isn't stated. However, in the Results, they note that some miRNAs may not actually act on the genes due to imperfect predictions, but FDR correction isn't mentioned. So the answer is not described. Wait, in the Discussion, they mention that in the miR-SNP analysis, the single CLASH-supported miR-SNP was found, but the pathways were tested using statistical overrepresentation. The article doesn't specify if they adjusted for multiple testing beyond that. So for question 6, the answer is not described. Putting it all together, the answers would be: 1. Tool: Not described 2. Version: Not described 3. Gene set libraries: GO, Reactome 4. Background gene list: Not described 5. Statistical test: Not described 6. FDR correction: Not described I need to make sure there's no mention in other sections. The Abstract and Results do mention pathways but not the methods. The Conflicts of Interest and Author Contributions sections don't help here. So the answers remain as above. 1. **What tool was used for pathway enrichment analysis?** Not described. The article does not specify the exact tool (e.g., DAVID, GSEA, Reactome GSA, etc.) used for pathway enrichment analysis. 2. **Was a tool version number provided?** Not described. No version number is mentioned. 3. **What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** GO (Gene Ontology) and Reactome. The article explicitly references GO cellular components (e.g., "MHC protein complex," "integral component of the luminal side of endoplasmic reticulum membrane") and Reactome (e.g., "interferon gamma signaling pathway"). 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, or a curated set) was used. 5. **What statistical test was used for enrichment analysis?** Not described. The article mentions "statistical overrepresentation tests" but does not specify the exact statistical test (e.g., hypergeometric test, Fisher’s exact test). 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 explicitly state whether FDR correction or another multiple testing correction method was applied. --- **Table Summary:** | Question | Answer | |----------|--------| | 1. Tool used | Not described | | 2. Tool version | Not described | | 3. Gene set library | GO, Reactome | | 4. Background gene list | Not described | | 5. Statistical test | Not described | | 6. FDR correction | Not described |