Alright, let's tackle this query step by step. The user has provided an abstract and sections from a scientific article about Ursolic Acid (UA) and its effects on gallbladder cancer cells. They want me to examine how pathway enrichment analysis was conducted, focusing on the Methods section but also considering other parts if necessary. First, I'll look for any mention of the tools used in the article. The abstract doesn't provide this info, so I need to check the detailed sections. In Table II, under Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, it's mentioned that the pathways listed are from KEGG, like hsa04064 for NF-κB signaling. Next, about the tool used, the article references KEGG, so I infer they might have used KEGG's own tools or perhaps another tool that interfaces with the KEGG database. However, the version isn't specified anywhere in the text provided, so I'll note that as not described. For the gene set library, since all pathways are labeled with 'hsa' followed by numbers, it's clear they're using KEGG pathways. So, the gene set is definitely KEGG. Regarding a background gene list, the article doesn't mention defining one, so I'll assume it wasn't described and default to that answer. Statistical test used: The tables show p-values, but there's no detail on which test was applied (like hypergeometric test or others). So, this is also not described. Lastly, false discovery rate correction isn't mentioned anywhere. The article doesn't discuss multiple testing corrections, so I'll note that as well. Putting it all together, the answers are based on what's explicitly stated and what's left unstated in the provided text. | Question | Answer | |----------|--------| | 1. What tool was used for pathway enrichment analysis? | Database for Annotation, Visualization and Integrated Discovery (DAVID) or another KEGG-related tool (not explicitly described). | | 2. Was a tool version number provided? | Not described. | | 3. What gene set library was queried (e.g., GO, KEGG, Reactome, or other)? | KEGG (Kyoto Encyclopedia of Genes and Genomes). | | 4. Was a background gene list defined for pathway enrichment analysis? | Not described. | | 5. What statistical test was used for enrichment analysis? | Not described. | | 6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis? | Not described. |