Okay, so I'm trying to figure out how to answer these questions about the pathway enrichment analysis from this scientific article. Let me read through the provided text carefully and see what information I can extract. First, the abstract mentions that they did GO and KEGG pathway analyses. In the discussion section, they talk more about the results of these analyses, like cell cycle and DNA replication pathways being significant. Looking at question 1: What tool was used for pathway enrichment analysis? The methods section isn't provided here, but in the abstract, they mention using Limma in R package for DEG screening. I don't see a specific tool named for pathway analysis, so maybe it's not described. Question 2: Version number of the tool. Since the tool itself isn't mentioned, there's no version number either. So probably not described. Question 3: Gene set libraries used. The abstract says they did GO and KEGG analyses, so those are the libraries queried. Question 4: Background gene list. I don't recall reading about a specific background list being defined. They used all the DEGs for analysis, but without more details, it's unclear if they used a particular background. Question 5: Statistical test used. The article doesn't specify which test was applied, like hypergeometric or something else. It just mentions pathway analysis was done. Question 6: False discovery rate correction. There's no mention of FDR or multiple testing corrections in the text provided. So probably not described. Putting it all together, I think most details about the methodology for pathway enrichment aren't specified in the article. | Question | Answer | |----------|--------| | 1. What tool was used for pathway enrichment analysis? | Not described. | | 2. Was a tool version number provided? | Not described. | | 3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)? | Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). | | 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. |