Okay, so I need to figure out how to answer these six questions about the pathway enrichment analysis from this scientific article. Let me start by reading through the abstract and the methods section carefully. First question: What tool was used for pathway enrichment analysis? Looking at the Methods section, it mentions two approaches—the tissue restricted gene enrichment analysis and another using the DAVID server. So, the tools are both the custom method they describe and the DAVID Bioinformatics Resources version 8.0. But since the question is about the tool, I should note both, but perhaps the primary one is DAVID. Second question: Was a tool version number provided? Yes, in Additional file 4, it references DAVID Bioinformatic Resources 6.8 server. Wait, that might be conflicting because elsewhere it says 8.0. Hmm, maybe I need to check again. In the Methods section under gene enrichment analysis, they mention using the DAVID server, and Additional file 14 cites version 6.8. So perhaps it's 6.8. Third question: What gene set library was queried? The article talks about GO terms, so Gene Ontology. Also, in Additional files like 3 and 4, they mention GO terms. I don't see any reference to KEGG or Reactome, so the answer is GO. Fourth question: Was a background gene list defined for pathway enrichment analysis? Yes, the article says that a list of 10,919 genes expressed in bovine skeletal muscle was used as the background. This is mentioned in Additional file 12 and referenced in the Methods section. Fifth question: What statistical test was used for enrichment analysis? The Methods don't specify the exact test, but they do mention using the DAVID server, which typically uses a modified Fisher's exact test or hypergeometric test. Since it's not explicitly stated, I should note that it's not described in the article. Sixth question: Was false discovery rate correction used to control the number of false positives? The Methods section does say that the significance of each enriched term was adjusted applying the Benjamini-Hochberg p-value correction, which is a type of FDR correction. So yes, FDR was used. 1. **Tool Used**: DAVID Bioinformatics Resources (version 6.8 as per Additional file 14) and custom tissue-restricted gene enrichment analysis. 2. **Version Number Provided**: Yes, version 6.8 for the DAVID server. 3. **Gene Set Library Queried**: Gene Ontology (GO). 4. **Background Gene List Defined**: Yes, a background list of 10,919 genes expressed in bovine skeletal muscle was used. 5. **Statistical Test Used**: Not explicitly described; typically, tools like DAVID use Fisher's exact or hypergeometric tests. 6. **FDR Correction Applied**: Yes, Benjamini-Hochberg correction was applied to control false positives.