To analyze how pathway enrichment analysis was conducted in the article, we'll extract and summarize relevant details:

1. **What tool was used for pathway enrichment analysis?**
   - The tool used is MAGMA (Multi-marker Analysis of GenoMic Annotation).

2. **Was a tool version number provided?**
   - No version number for MAGMA is provided.

3. **What gene set library was queried (e.g., GO, KEGG, Reactome or other)?**
   - The specific gene set libraries are not described in the article. However, it mentions that gene expression data from GTEx and PheWAS catalog were used, which may imply some predefined pathways related to gene expressions.

4. **Was a background gene list defined for pathway enrichment analysis?**
   - A background gene list is not explicitly mentioned as being defined separately; however, the article indicates genes with significant associations (P < 5 × 10^-8) are considered.

5. **What statistical test was used for enrichment analysis?**
   - The specific statistical test used by MAGMA for pathway enrichment isn't detailed in the article. Generally, MAGMA uses a linear model to assess gene-set enrichment but this particular aspect is not described here.

6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?**
   - False discovery rate (FDR) correction is mentioned as being applied to adjust for multiple comparisons in the context of gene expression and associations, though it's not specified if FDR was specifically used within the MAGMA pathway analysis itself.

Here’s how this information would be organized into a table:

| Question                                                                 | Answer                               |
|--------------------------------------------------------------------------|--------------------------------------|
| What tool was used for pathway enrichment analysis?                      | MAGMA                                |
| Was a tool version number provided?                                       | Not described                        |
| What gene set library was queried (e.g., GO, KEGG, Reactome or other)?    | Not described; uses GTEx and PheWAS data|
| Was a background gene list defined for pathway enrichment analysis?       | Not explicitly described             |
| What statistical test was used for enrichment analysis?                   | Not described (generally involves linear model) |
| Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis? | FDR correction is mentioned, but not specifically for MAGMA analysis |

This table provides a concise summary based on the available information.