Thinking... We need to examine article: "Ursolic acid isolated from Isodon excision (C) inhibits the invasive capacity of gallbladder cancer cells". The methods section we saw earlier. We need details about pathway enrichment analysis. Let's locate in methods: We saw: "Effects of UA on GBC-SD cells are at least in part via NF-κB and Akt signaling pathways" - They used PCR array to evaluate expression of 168 genes. Then they mention: "KEGG pathway analysis of the 24 differentially expressed genes was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID)". Thus the tool: Database for Annotation, Visualization and Integrated Discovery (DAVID). They also used KEGG pathway enrichment analysis. They mention using "Database for Annotation, Visualization and Integrated Discovery" (DAVID). Also, they mention "KEGG pathway enrichment analysis" within results. But do they mention using a particular version of DAVID? I don't see a version number. Let's check. In the methods: They say: "KEGG pathway analysis of the 24 differentially expressed genes was performed using the Database for Annotation, Visualization and Integrated Discovery ([78]15,[79]16)." But they don't give version. They don't mention background gene list. They mention using "P-value" for each pathway with threshold <0.05. They mention: "The differentially expressed genes were significantly associated with NF-κB, TNF, PI3K-Akt and other signaling pathways." In table II, they list pathways and P-values. The methods section didn't describe which statistical test: likely the hypergeometric or Fisher exact test implemented by DAVID. But they didn't mention test. They mention: "According to KEGG pathway enrichment analysis, the differentially expressed genes were significantly associated with NF-κB, TNF, PI3K-Akt and other signaling pathways". Did they mention hypergeometric test? Not explicitly. Also, multiple testing correction: They mention P-values but no mention of FDR. They didn't mention "Benjamini-Hochberg" etc. So multiple testing correction is Not described. Also, custom background gene list: Not described. Also, the tool version: Not described. Also, gene set library used: KEGG. They didn't mention GO or others. But check if any other tool used: They also mention "Database for Annotation, Visualization and Integrated Discovery" (DAVID). They also mention "KEGG pathway enrichment analysis" using "DAVID". So we have tool: DAVID. Gene set library: KEGG. We should check if there is any other mention: In methods: They say: "KEGG pathway analysis of the 24 differentially expressed genes was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID)". So that's all. They didn't mention "GSEA" or "Enrichr". Also, they used "Database for Annotation, Visualization and Integrated Discovery" (DAVID). That's the tool. So answer: tool: DAVID. No version described. Gene set libraries: KEGG. Custom background: Not described. Statistical test: Not described. Multiple testing correction: Not described. Wait: For enrichment analysis they might mention the method: "The P-value was used as the significance threshold and pathways with P<0.05 were considered statistically significant." But they didn't mention multiple testing correction. So "No" for multiple testing correction. But the table must have columns: Tool used for pathway enrichment analysis; Enrichment tool version(s) described; Which gene set libraries were used; Custom/background gene list used? Options Yes, No, Not described; What statistical test(s) used; Was multiple testing correction / FDR applied? Only "Yes" if mention. So fill table. But we need to verify if they used any other tool. The article mentions "KEGG pathway enrichment analysis" using DAVID. Also they mention "KEGG pathway enrichment analysis" referencing Table II. Did they also use "Database for Annotation, Visualization and Integrated Discovery (DAVID) (https://david.ncifcrf.gov)". Let's search in article for "DAVID". The Methods mention "KEGG pathway analysis ... using the Database for Annotation, Visualization and Integrated Discovery (DAVID)" as we saw. But they also mention earlier: "KEGG pathway analysis of the 24 differentially expressed genes was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) (see references [78]15, [79]16)." So only tool: DAVID. Also mention "Database for Annotation, Visualization and Integrated Discovery" (DAVID). The version of DAVID not given. The gene set libraries: KEGG. Now we need to produce a table summarizing six questions. Let's list columns: 1. Tool used for pathway enrichment analysis 2. Enrichment tool version(s) described 3. Gene set libraries used 4. Custom or specific background gene list used? (Yes, No, Not described) 5. Statistical test(s) used in enrichment analysis 6. Multiple testing correction / FDR applied to enrichment analysis Now answer each. For tool used: DAVID. For version: Not described. For gene set libraries: KEGG. For custom background: Not described. For statistical test(s): Not described (maybe hypergeometric test by default but not stated). For multiple testing correction: Not described. Provide table. But we need to check if the article mentions any specific background gene list. They might not. So answer Not described. Also, we might double-check if they mention "FDR" etc. They didn't. They mention P-values. So "No". Also, they might mention "hypergeometric test" or "Fisher's exact test". Not present. Thus output table. Let's craft. ...done thinking. | Question | Answer | |----------|--------| | **What tool was used for pathway enrichment analysis?** | DAVID | | **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 |