Thinking... We need to extract only what is explicitly reported. We must answer 6 questions in table format. Let's parse the article to identify details about pathway enrichment analysis. The Methods section says: "We performed KEGG enrichment analysis by using the WebGestalt online platform (http://www.webgestalt.org/) and default setting. The threshold of P-value 0.05 and fold change 1.5 were used for DEGs and 3-fold change for the comparison between DEGs and the background genes." Also later in results: "KEGG enrichment analysis" is repeated. They mention "The KEGG enrichment analysis results" again. Also they mention "We obtained different conclusions" and used "KEGG enrichment analysis results, which listed 'AMPH addiction' as one of the top 10 significantly enriched KEGG pathways." Also in results: "To reveal gene expression changes and related pathways ... KEGG enrichment analysis results." Also they mention "The KEGG enrichment analysis results, which listed “AMPH addiction” as one of the top 10 significantly enriched KEGG pathways." Also earlier: "The analysis of the top 10 DEGs in schizophrenia and healthy samples revealed that FOS and FOSB (which are involved in the AMPH addiction pathway) ... Protein functional network analysis revealed proteins closely interacting with FOS that were also involved in the AMPH addiction pathway. ... KEGG enrichment analysis results, which listed 'AMPH addiction' as one of the top 10 significantly enriched KEGG pathways." Also they mention "To discover gene expression changes, we used WebGestalt for KEGG enrichment." Let me check the exact text: In Methods section: "We performed KEGG enrichment analysis by using the WebGestalt online platform (http://www.webgestalt.org/) and default setting. The threshold of P-value 0.05 and fold change 1.5 were used for DEGs and 3-fold change for the comparison between DEGs and the background genes." Also they say: "We performed KEGG enrichment analysis." So the tool: WebGestalt. Also they mention "We performed pathway functional network analysis using PANTHER, STRING? Wait: They mention earlier: "We performed pathway functional network analysis using PPI network" maybe? Let's search. The text: "Protein functional network analysis" - earlier: "Protein functional network analysis revealed proteins closely interacting with FOS that were also involved in the AMPH addiction pathway." But the methods for that may involve "STRING" or "PPI" database. But we need only enrichment analysis tools. For pathway enrichment, the only tool explicitly mentioned is WebGestalt. They also mention "KEGG enrichment analysis" which is the database. They may mention "WebGestalt" and "KEGG". They may mention "PCA" or "GSEA" but not. Additionally, they mention "We performed KEGG enrichment analysis by using the WebGestalt online platform." So the tool used: WebGestalt. Was enrichment tool version described? The article says "Not described." Because no version number is given for WebGestalt. Which gene set libraries were used? They used "KEGG". They mention "GO" or "Reactome"? Let's search. The article text: "We performed KEGG enrichment analysis." They also mention "The KEGG enrichment analysis results, which listed 'AMPH addiction' as one of the top 10 significantly enriched KEGG pathways." They didn't mention GO or Reactome or other gene set libraries. Also, they used "WebGestalt" which is an online enrichment platform that supports multiple libraries. They used KEGG specifically. They didn't mention GO or others. Custom background gene list? The Methods says: "The threshold of P-value 0.05 and fold change 1.5 were used for DEGs and 3-fold change for the comparison between DEGs and the background genes." That sentence may be ambiguous: "fold change 1.5 were used for DEGs and 3-fold change for the comparison between DEGs and the background genes." But that likely refers to the thresholds for DEGs selection, not background gene list. They didn't mention custom background list. So answer: Not described. Statistical tests: They didn't mention the specific test for enrichment. They used "WebGestalt" default. WebGestalt uses hypergeometric test by default. But the article doesn't mention that. It just says "default setting." So we need to list tests linked to enrichment. There's no explicit mention. So answer "Not described" maybe. However we might consider "hypergeometric test" as default but not described. So "Not described". Multiple testing correction: They mention "the threshold of P-value 0.05" but not FDR. In the article: "The threshold of P-value 0.05 and fold change 1.5 were used for DEGs and 3-fold change for the comparison between DEGs and the background genes." Also earlier: "DEGs were considered significant if they had a false discovery rate (FDR) of < 0.05." Wait earlier in Methods: "DEGs were defined as having a false discovery rate (FDR) of <0.05 and fold change (FC) ≥1.5 or ≤-1.5." So they used FDR for differential expression, not enrichment. For enrichment, they said "P-value < 0.05" in the results for pathway enrichment: "The top 10 significantly enriched KEGG pathways." But no mention of multiple testing correction. Thus answer for multiple testing correction: Not described. Let's construct the table. Columns: 1. Tool used for pathway enrichment analysis 2. Tool version(s) described 3. Gene set libraries used 4. Custom background list used? Options Yes, No, Not described 5. Statistical tests used in enrichment analysis 6. Multiple testing correction / FDR applied? Yes/No/Not described But we should combine them: each row could be for each tool. Since only one tool (WebGestalt). So only one row. Thus: Tool used: WebGestalt Tool version(s) described: Not described Gene set libraries used: KEGG Custom background list used: Not described Statistical test(s): Not described Multiple testing correction / FDR applied: Not described Wait, for the last column: "Was multiple testing correction / FDR applied to enrichment analysis? Only answer "Yes" if the article explicitly mentions FDR, false discovery rate, Benjamini–Hochberg, or a named correction method for the enrichment analysis. A p-value threshold alone is not sufficient." The article does not mention FDR for enrichment. So answer "Not described". Now ensure that we only list details explicitly reported. So yes. Let's produce the table: | Question | Answer | But the instructions say: "Provide output in table format." We have 6 questions. So maybe produce a table with 6 rows? Each row with the question and answer. Or produce a table with columns for each of the 6 question categories? Actually the prompt: "Please answer the following 6 questions. If more than one tool, method, or database is used, list all of them separately. ... Provide output in table format." So we need a table with 6 rows, each row corresponding to a question, and columns for "Question" and "Answer" maybe. Or each column for each aspect? We need to produce a table format that lists tool, version, gene set libraries, custom background, statistical tests, multiple testing correction. So maybe we produce a table with two columns: 'Category' and 'Detail'. Given the instructions: "What tool was used for pathway enrichment analysis?: List all tools or software packages used (e.g., DAVID, GSEA, Enrichr, etc.) that are explicitly mentioned in the article for enrichment analysis. Do not include tools used only for preprocessing (e.g., Salmon). Were enrichment tool version(s) described?: List the version numbers associated with each enrichment tool, if reported. Which gene set libraries were used?: Identify all gene set libraries or databases the authors queried (e.g., GO, KEGG, Reactome, MSigDB, etc.). Only include what's actually stated in the article. Does the article describe using a custom or specific background gene list for enrichment analysis? Your options include Yes, No or Not described. What statistical test(s) were used in enrichment analysis?: State the name(s) of the statistical test(s) used for enrichment analysis (e.g., hypergeometric test, Fisher's exact test). Only include tests linked to enrichment. Was multiple testing correction / FDR applied to enrichment analysis?: Only answer "Yes" if the article explicitly mentions FDR, false discovery rate, Benjamini-Hochberg, or a named correction method for the enrichment analysis. A p-value threshold alone is not sufficient. Provide output in table format." Thus we need a table with six rows, each row corresponding to the answer for each question. So columns: Question, Answer. So we can create: | Question | Answer | | What tool was used for pathway enrichment analysis? | WebGestalt | | Were enrichment tool version(s) described? | Not described | | Which gene set libraries were used? | KEGG | | Does the article describe using a custom or specific background gene list for enrichment analysis? | Not described | | What statistical test(s) were used in enrichment analysis? | Not described | | Was multiple testing correction / FDR applied to enrichment analysis? | Not described | But the instructions say: "If more than one tool, method, or database is used, list all of them separately." There's only one tool. So "WebGestalt" singular. Also "Not described" is an answer for version. For tests, if not described: "Not described". For multiple testing correction: Not described. Yes. Let's ensure no missing details: The article didn't mention a specific background gene list. So "Not described". Also the article didn't mention the statistical test used; so "Not described". Now produce the table. ...done thinking. | Question | Answer | |---|---| | What tool was used for pathway enrichment analysis? | WebGestalt | | Were enrichment tool version(s) described? | Not described | | Which gene set libraries were used? | KEGG | | Does the article describe using a custom or specific background gene list for enrichment analysis? | Not described | | What statistical test(s) were used in enrichment analysis? | Not described | | Was multiple testing correction / FDR applied to enrichment analysis? | Not described |