Alright, I need to figure out how to answer these six questions about the pathway enrichment analysis from the provided article. Let me go through each question one by one and see what information I can extract. 1. **What tool was used for pathway enrichment analysis?** - Looking at the abstract and the discussion sections, it mentions "mummichog software" was used to predict molecules from pathways. So, I think Mummichog is the tool here. 2. **Was a tool version number provided?** - I don't recall seeing any version numbers mentioned in the text. It just refers to "mummichog software," but no specific version is noted. 3. **What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** - The article mentions using KEGG for matching compounds. For example, it says "Matched Compound (KEGG by mummichog)" in the additional files section and discusses pathways like retinol metabolism which are part of KEGG. 4. **Was a background gene list defined for pathway enrichment analysis?** - The text doesn't specify whether a background list was used. It just describes using Mummichog without detailing the parameters or inputs beyond the data itself. 5. **What statistical test was used for enrichment analysis?** - The article doesn't explicitly mention which statistical test was applied, like hypergeometric test or others. It only states that pathways were significant but doesn't specify the method. 6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** - There's no indication in the text about using FDR correction for the pathway analysis itself, though they might have used some multiple testing correction elsewhere in their analysis. Here are the answers based on the analysis: 1. **Tool Used**: Mummichog software 2. **Version Number**: Not described 3. **Gene Set Library**: KEGG 4. **Background Gene List**: Not described 5. **Statistical Test**: Not described 6. **FDR Correction**: Not described These answers reflect the information available in the provided text, highlighting where details were absent.