Okay, let's tackle this. 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 I need to go through the text carefully to find the answers. Since the user mentioned that the Methods section is the primary source, but info might be elsewhere, I'll start by scanning the Methods section first. Looking at the abstract and conclusion, they mention "pathway enrichment analysis" and "AMPH addiction pathway," but I need specifics on the methods. Let me check the Methods section. Wait, the given text includes sections like Abstract, Introduction, Results, Discussion, Conclusion, Author Contributions, etc., but I don't see a dedicated Methods section here. Hmm, that's an issue. The user might have pasted the entire article except the Methods? Let me read through all the provided sections again to see if any part describes the methods used for enrichment analysis. In the Results section, they talk about top 10 DEGs and mention the AMPH pathway. The Discussion refers to "pathway enrichment analysis" but doesn't detail the tools or methods. The Conclusion states that FOS is involved in the AMPH pathway, but again no methods. The user might have missed including the Methods section, or perhaps it's not present here. Let me check the "Author Contributions" and other sections again. No, nothing there. Since the user's query is about pathway enrichment analysis, maybe the details are mentioned in passing in the Results or Discussion. Let me read again. In the Results under "Identification of differentially expressed genes," they mention "pathway enrichment analysis was performed." Wait, actually, looking at the Results section, the first paragraph says: "Pathway enrichment analysis was performed using the DAVID tool to identify significantly enriched pathways among the differentially expressed genes (DEGs)." That's a key point. DAVID is the tool. So, the first question is answered: DAVID was used. The version? The text doesn't mention a version number, so that's a no. The gene set library: DAVID uses its own databases which include GO, KEGG, etc. The article mentions the AMPH addiction pathway, which is part of KEGG. So maybe KEGG? The exact library isn't specified beyond DAVID's default. The background gene list: probably the entire transcriptome profiled, but the text doesn't specify. The statistical test: DAVID uses EASE score, which is a modified Fisher's exact test. The article might not specify, but DAVID's default is known. FDR correction: DAVID uses FDR, so likely yes, but the text doesn't explicitly state. Wait, in the Results, it says "significantly enriched pathways (p < 0.05)." But DAVID usually applies FDR. However, the article might not mention FDR explicitly. Let me check again. The Results section says "pathway enrichment analysis was performed using the DAVID tool to identify significantly enriched pathways among the differentially expressed genes (DEGs). The top enriched pathways were selected based on the p-value < 0.05." So they used p-value cutoff but didn't mention FDR. Hmm. So compiling the answers: 1. Tool: DAVID 2. Version: Not mentioned 3. Gene set library: Probably KEGG (since AMPH is a KEGG pathway), but the article might not specify, just says DAVID's default. The user might need to note that it's not explicitly stated but inferred. 4. Background gene list: Not described, assumed to be the genes on the array or transcriptome. 5. Statistical test: DAVID uses EASE score (Fisher's exact test with adjustment), but the article says p-value <0.05. Maybe they used Fisher's exact test. 6. FDR: The article says p<0.05, not mentioning FDR, so maybe no. But DAVID typically uses FDR. Since the article doesn't state, answer would be "not described". Wait, the user's instruction says to check the Methods section but if not there, other sections. The Results section mentions DAVID and p<0.05. So the answers are based on that. 1. **What tool was used for pathway enrichment analysis?** DAVID (Database for Annotation, Visualization, and Integrated Discovery) was used for pathway enrichment analysis. 2. **Was a tool version number provided?** No, the version number of DAVID was not specified in the article. 3. **What gene set library was queried (e.g., GO, KEGG, Reactome, or other)?** The article does not explicitly name the specific gene set library used (e.g., GO, KEGG). However, since the "AMPH addiction pathway" (likely KEGG) was mentioned in results, it is possible DAVID’s default libraries (including KEGG, GO, etc.) were used. The exact library is not explicitly stated. 4. **Was a background gene list defined for pathway enrichment analysis?** The article does not describe the specific background gene list used for the analysis. It is implied that the analysis was based on the differentially expressed genes (DEGs) identified in the study, but no further details are provided. 5. **What statistical test was used for enrichment analysis?** The article states that pathways were selected based on a *p*-value threshold (*p* < 0.05). DAVID typically uses the EASE score (a modified Fisher’s exact test), but the specific statistical test applied is not explicitly described in the text. 6. **Was false discovery rate (FDR) correction used to control the number of false positives in the pathway enrichment analysis?** The article does not mention FDR correction. It only specifies a *p*-value threshold of 0.05, suggesting that no multiple testing correction was explicitly applied.