Okay, let's tackle these questions about the pathway enrichment analysis in the study. First, I need to look through the Methods section and other relevant parts of the article. 1. **Tool used for pathway enrichment analysis**: The Methods mention that "Ingenuity Pathway Analysis (IPA) was applied to recognise gene pathways associated with vitamin A supplementation." So the tool is IPA. 2. **Tool version number**: The article doesn't specify the version of IPA. It just says "Ingenuity Pathway Analysis," so the version is not described. 3. **Gene set library queried**: IPA typically uses its own curated database of pathways, which is a combination of various sources. However, the article doesn't explicitly mention which specific library (like GO, KEGG, Reactome) was used. It just refers to "canonical pathways" as mentioned in the Results. Since the question asks for the library, and the article doesn't specify, it's not described. 4. **Background gene list defined**: The Methods don't mention whether a specific background gene list was used. The analysis was on the differentially expressed transcripts identified from the microarray. Without explicit mention, this is not described. 5. **Statistical test for enrichment analysis**: The article states that genes were identified as differentially expressed with P < 0.05, but for the pathway analysis, it's not clear what specific test was used. The Results mention "canonical pathways (P < 0.05)", but the exact statistical method isn't detailed. So this is not described. 6. **False discovery rate correction**: The Methods mention using a P-value threshold of <0.05 for differentially expressed transcripts, but there's no mention of FDR correction for the pathway analysis. Therefore, it's not described. 1. **Tool used for pathway enrichment analysis**: **Ingenuity Pathway Analysis (IPA)** 2. **Tool version number provided?** **Not described** 3. **Gene set library queried?** **Not described** (The article refers to "canonical pathways" but does not specify the gene set library, such as GO, KEGG, or Reactome.) 4. **Background gene list defined?** **Not described** 5. **Statistical test used for enrichment analysis?** **Not described** (The article mentions pathways with *P < 0.05* but does not specify the statistical test used for enrichment analysis.) 6. **False discovery rate (FDR) correction used?** **Not described** --- ### Summary Table | Question | Answer | |----------|--------| | 1. Tool used for pathway enrichment analysis | Ingenuity Pathway Analysis (IPA) | | 2. Tool version number provided? | Not described | | 3. Gene set library queried? | Not described | | 4. Background gene list defined? | Not described | | 5. Statistical test used for enrichment analysis? | Not described | | 6. False discovery rate correction used? | Not described |