Okay, so I'm trying to figure out how the authors conducted their pathway enrichment analysis based on this article. Let me go through each question step by step. 1. **What tool was used for pathway enrichment analysis?** - Looking at the Methods section under "De novo assembly and functional annotation," it says they used Blast all software against the KEGG database. So, I think Blast all is the tool here. 2. **Was a tool version number provided?** - The text mentions Blast all software but doesn't specify any version numbers. So, no, it's not described. 3. **What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** - It clearly states they used the KEGG database for pathway annotation. So, the answer is KEGG. 4. **Was a background gene list defined for pathway enrichment analysis?** - The article doesn't mention anything about using a specific background gene list. They just mapped DEGs to KEGG pathways without referencing a particular background set. 5. **What statistical test was used for enrichment analysis?** - In the Methods, they mention using Q-value ≤0.05 for pathway enrichment. Q-value is a measure that accounts for multiple testing, typically involving permutation tests or other methods, but the exact test isn't specified beyond the threshold. 6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** - The article doesn't explicitly mention FDR correction. They talk about Q-value thresholds, which might imply some form of correction, but it's not clearly stated whether FDR was applied specifically. | Question | Answer | |----------|--------| | 1. What tool was used for pathway enrichment analysis? | Blast all software | | 2. Was a tool version number provided? | Not described | | 3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)? | KEGG | | 4. Was a background gene list defined for pathway enrichment analysis? | Not described | | 5. What statistical test was used for enrichment analysis? | Q-value ≤0.05 | | 6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis? | Not explicitly mentioned, but Q-value implies some correction | The authors used Blast all software against the KEGG database without specifying a version or background gene list. They set a statistical threshold at Q-value ≤0.05 for pathway enrichment, suggesting possible FDR-based correction but didn't confirm it explicitly.