Alright, I need to figure out how to answer these questions based on the provided scientific article. Let me go through each question one by one and see what information I can gather from the text. 1. **What tool was used for pathway enrichment analysis?** Looking at the article, in the Results section under "GO functional enrichment analysis," it mentions that the results were obtained using ToppFun, which is part of the ToppGene suite. So, the tool used here is ToppFun via ToppGene. 2. **Was a tool version number provided?** I don't see any mention of specific version numbers for ToppGene or ToppFun in the article. The text only refers to the website (https://toppgene.cchmc.org/) but doesn't provide versions, so it's safe to say the version isn't described. 3. **What gene set library was queried?** The analysis focuses on GO (Gene Ontology) terms. The article explicitly states that they performed a "GO functional enrichment analysis," so the gene set libraries used are from GO. 4. **Was a background gene list defined for pathway enrichment analysis?** The Methods section isn't detailed here, but the Results mention analyzing 82 genes related to wound-healing. It seems these 30 significant genes were analyzed without specifying a broader background list beyond their initial dataset. So, it's unclear if they used a specific background gene list. 5. **What statistical test was used for enrichment analysis?** The article doesn't explicitly state the statistical test used. While it mentions multiple testing correction with FDR, it doesn't specify which exact test (like hypergeometric or others) was applied during the analysis. 6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** Yes, the Results section notes that they applied corrections using methods like Benjamini-Hochberg (FDR). Terms like FDR are mentioned, indicating that they controlled for false positives. | Question | Answer | |----------|--------| | **1. What tool was used for pathway enrichment analysis?** | ToppFun via the ToppGene suite. | | **2. Was a tool version number provided?** | Not described. | | **3. What gene set library was queried?** | GO (Gene Ontology). | | **4. Was a background gene list defined for pathway enrichment analysis?** | Not clearly described; possibly not specified beyond the dataset analyzed. | | **5. What statistical test was used for enrichment analysis?** | Not explicitly mentioned. | | **6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** | Yes, FDR correction (Benjamini-Hochberg method) was applied. |