Okay, let's tackle these questions about the pathway enrichment analysis in the article. I need to go through the Methods section and other parts to find the answers. First question: What tool was used for pathway enrichment analysis? The article mentions "mummichog prediction" in the Discussion, but the actual pathway analysis is referred to in the Methods. Wait, in the Results section under "Pathway enrichment analysis," they say they used Mummichog. Let me check the Methods. The Methods section says, "Pathway enrichment analysis was conducted using Mummichog (version 2.0)." So the answer to question 1 is Mummichog. Question 2: Was a tool version number provided? The Methods explicitly states "Mummichog (version 2.0)," so yes, version 2.0. Question 3: What gene set library was queried? The article mentions KEGG in the Discussion when talking about RDH5, but in the Methods, when describing the pathway analysis, it says "Mummichog was used to map the features to KEGG pathways." So the library is KEGG. Question 4: Was a background gene list defined? The Methods doesn't mention defining a specific background list. The analysis was done on the features identified in the metabolomics data. The article doesn't specify if they used all detected features or a subset, but there's no mention of a separate background list. So probably not described. Question 5: What statistical test was used for enrichment analysis? The Methods says "a hypergeometric test was used to determine enrichment of features in pathways." So the answer is hypergeometric test. Question 6: Was FDR correction used? The Methods states "false discovery rate (FDR) correction was applied to the p-values." So yes, they used FDR correction. Let me double-check each point. The tool is Mummichog version 2.0, library is KEGG, hypergeometric test, and FDR correction. The background gene list isn't mentioned, so it's not described. All answers seem covered. | **Question** | **Answer** | |--------------|------------| | 1. What tool was used for pathway enrichment analysis? | **Mummichog** | | 2. Was a tool version number provided? | **Yes, version 2.0** | | 3. What gene set library was queried? | **KEGG pathways** | | 4. Was a background gene list defined? | **Not described** | | 5. What statistical test was used for enrichment analysis? | **Hypergeometric test** | | 6. Was false discovery rate correction used? | **Yes** |