<think>
Okay, let's tackle this question step by step. The user wants me to examine the pathway enrichment analysis conducted in the provided scientific article and answer six specific questions. Let me start by carefully reading through the Methods section and other relevant parts of the article.

First, the user is asking about the tools used for pathway enrichment analysis. In the Methods section under "Gene enrichment analysis," the authors mention using the DAVID server. So the answer to question 1 is DAVID. 

Next, question 2 asks if a tool version number was provided. Looking at the text, they just say "DAVID server" without specifying a version. So the answer here is no, the version isn't provided.

For question 3, the gene set library queried. The DAVID server is known to use Gene Ontology (GO) terms, and the article specifically mentions "Gene Ontology by gene" in Additional file 1. They also refer to GO terms in the results. So the answer is GO.

Question 4 is about the background gene list. The article states that the background list was defined as 10,919 genes expressed in bovine skeletal muscle from EMBL-EBI Expression Atlas. This is detailed in Additional file 12. So yes, the background gene list was defined.

Question 5 asks about the statistical test used. The Methods section mentions that the significance of each enriched term was adjusted using the Benjamini-Hochberg p-value correction. However, the actual statistical test for enrichment isn't explicitly named. The DAVID server typically uses hypergeometric tests or Fisher's exact tests, but the article doesn't specify which one. So the answer here is not described.

Lastly, question 6 about false discovery rate correction. The article does mention that the Benjamini-Hochberg correction was applied, which is a method to control the false discovery rate. So the answer is yes.

Putting all this together, I need to make sure each answer corresponds correctly to the questions and that I haven't missed any details. The key points are in the Methods section and Additional files 12 and 14. The DAVID server was used with GO terms, a background list was defined, Benjamini-Hochberg correction was applied for FDR, but the specific statistical test isn't mentioned. The version of DAVID isn't provided either.
</think>

Here are the answers to the questions based on the provided article:

1. **What tool was used for pathway enrichment analysis?**  
   **DAVID server** (Database for Annotation, Visualization and Integrated Discovery).  

2. **Was a tool version number provided?**  
   **Not described** (The article does not specify a version number for DAVID).  

3. **What gene set library was queried?**  
   **Gene Ontology (GO)**. The authors explicitly mention GO terms in the analysis (e.g., "Gene Ontology by gene" in Additional file 1 and "GO terms" in Additional file 14).  

4. **Was a background gene list defined for pathway enrichment analysis?**  
   **Yes**. The background gene list was defined as **10,919 genes reported as expressed in bovine skeletal muscle** by the EMBL-EBI Expression Atlas (Additional file 12).  

5. **What statistical test was used for enrichment analysis?**  
   **Not described** (The article states that significance was adjusted using the Benjamini-Hochberg p-value correction but does not specify the underlying statistical test, such as hypergeometric or Fisher’s exact test).  

6. **Was false discovery rate correction used?**  
   **Yes**. The Benjamini-Hochberg p-value correction was applied to adjust the significance of enriched terms (Methods section and Additional file 2).  

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### Summary Table:
| Question | Answer |
|----------|--------|
| 1. Tool used for pathway enrichment analysis | **DAVID server** |
| 2. Tool version provided? | **Not described** |
| 3. Gene set library queried | **Gene Ontology (GO)** |
| 4. Background gene list defined? | **Yes** |
| 5. Statistical test used | **Not described** |
| 6. False discovery rate correction used? | **Yes** |