Alright, so I need to figure out how to answer these six questions about the pathway enrichment analysis from this scientific article. Let me go through each question one by one and see where the information is in the text. 1. **What tool was used for pathway enrichment analysis?** Looking at the Methods section under "Functional enrichment analysis," it mentions that DAVID version 6.8 and WebGestalt 2017 were used. So both tools were utilized. 2. **Was a tool version number provided?** Yes, in the same section, DAVID is specified as version 6.8 and WebGestalt as 2017. 3. **What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** The article says that both DAVID and WebGestalt were used for Gene Ontology (GO) terms and KEGG pathways. So they looked into both GO and KEGG. 4. **Was a background gene list defined for pathway enrichment analysis?** In the Methods, it's mentioned that the Bos taurus genome was used as the background for both analyses. So yes, a background was defined. 5. **What statistical test was used for enrichment analysis?** The article doesn't specify any particular statistical test beyond using FDR correction and p-values adjusted with FDR. It just says ORA (Overrepresentation Enrichment Analysis) was performed by DAVID, but the exact test isn't detailed. 6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** Yes, both DAVID and WebGestalt analyses were done with an FDR of 5%. Putting it all together, I think I've covered each point as per the information given. | Question | Answer | |----------|--------| | **1. What tool was used for pathway enrichment analysis?** | DAVID version 6.8 and WebGestalt 2017. | | **2. Was a tool version number provided?** | Yes, versions are specified as DAVID v6.8 and WebGestalt 2017. | | **3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** | Gene Ontology (GO) terms and KEGG pathways. | | **4. Was a background gene list defined for pathway enrichment analysis?** | Yes, the Bos taurus genome was used as the background. | | **5. What statistical test was used for enrichment analysis?** | Not explicitly described beyond FDR correction. | | **6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** | Yes, with a 5% FDR threshold. | This table summarizes the key details about how pathway enrichment analysis was conducted in the article.