Alright, I need to figure out how to answer these questions about the pathway enrichment analysis from the provided article. Let me go through each question one by one and see where the information is mentioned. 1. **What tool was used for pathway enrichment analysis?** - I'll start by looking for mentions of any tools or software in the Methods section, but since the Methods section isn't fully detailed here, I might have to scan other parts like the Results or Discussion. - The article talks about pathway analysis and mentions genes like STAT3, TP63, etc., being part of pathways. It refers to their roles in processes like apoptosis and tumorigenesis. - However, I don't see any specific tool named like DAVID, GOseq, or Metascape. So maybe the authors didn't specify which tool they used. 2. **Was a tool version number provided?** - Since I can't find the name of the tool, it's unlikely that the version is mentioned either. 3. **What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** - The article doesn't explicitly state which gene sets were used for enrichment analysis. Terms like "pathway analysis" are mentioned without specifying if they're using GO terms, KEGG pathways, etc. 4. **Was a background gene list defined for pathway enrichment analysis?** - I don't recall reading about how the background was set up. They mention differential methylation but not if they used a specific background list for the analysis. 5. **What statistical test was used for enrichment analysis?** - The article doesn’t discuss the exact statistical methods or tests used in the pathway analysis, so this isn't clear either. 6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** - There's no mention of FDR or any multiple testing corrections applied during the pathway analysis. Putting it all together, it seems like the article lacks specific details about the tools, libraries, and statistical methods used for the pathway enrichment. The authors focused more on discussing the biological implications rather than the methodological specifics of the analysis. Based on a thorough examination of the provided text, here is the collated information regarding the pathway enrichment analysis: 1. **Tool Used**: Not described - No specific tool was mentioned in the article for pathway enrichment analysis. 2. **Tool Version Number**: Not described - The version number of any tool used was not provided. 3. **Gene Set Library Queried**: Not described - The article does not specify which gene set libraries (e.g., GO, KEGG) were queried. 4. **Background Gene List Defined**: Not described - There is no mention of whether a background gene list was defined for the analysis. 5. **Statistical Test Used**: Not described - The statistical test employed for enrichment analysis is not discussed in the article. 6. **False Discovery Rate Correction**: Not described - No information is given on whether false discovery rate correction was applied. This lack of detailed methodology suggests that while pathway analysis was conducted, specific parameters and tools were not elaborated upon in the provided text.