Certainly! Here is an examination of how pathway enrichment analysis was conducted based on the provided article information:

1. **Tool Used for Pathway Enrichment Analysis**: 
   - The DAVID Bioinformatic Resources 6.8 server was used.

2. **Tool Version Number Provided**:
   - Yes, version number 6.8 is specified.

3. **Gene Set Library Queried**:
   - Gene Ontology (GO) terms were queried as indicated by the presence of GO term enrichment in the additional files and results sections.

4. **Background Gene List Defined**:
   - A background gene list was defined using a set of 10,919 genes reported as expressed in bovine skeletal muscle from the EMBL-EBI Expression Atlas (as noted in Additional file 12).

5. **Statistical Test Used for Enrichment Analysis**:
   - The Benjamini-Hochberg p-value correction method was used to adjust significance levels during enrichment analysis.

6. **False Discovery Rate Correction**:
   - Yes, false discovery rate correction was applied using the Benjamini-Hochberg method.

This summary can be collated into a table for easier reference:

| Question | Answer |
|----------|--------|
| Tool Used for Pathway Enrichment Analysis | DAVID Bioinformatic Resources 6.8 server |
| Tool Version Number Provided | Yes, version 6.8 |
| Gene Set Library Queried | GO (Gene Ontology) |
| Background Gene List Defined | Yes, from EMBL-EBI Expression Atlas (10,919 genes) |
| Statistical Test Used for Enrichment Analysis | Benjamini-Hochberg p-value correction |
| False Discovery Rate Correction Used | Yes |

This information was extracted and interpreted based on the provided details. If further clarification is needed or additional sections of the article are referenced, adjustments may be necessary.