<think>
Okay, let me try to figure out the answers to these questions based on the provided text. 

First, the user is asking about the pathway enrichment analysis in the scientific article. They want specific details from the Methods section and possibly other sections.

1. **What tool was used for pathway enrichment analysis?**
Looking through the Methods section, under the "Statistics" part, the authors mention using R (version 3.0.2) for descriptive statistics. However, for pathway enrichment analysis, they mention "gene annotations were obtained from Vectorbase using BioMart" and then categorizing genes into functional groups like apoptosis, chemosensory response, etc. The actual enrichment analysis seems to involve comparing functional subsets to all coding genes using hypergeometric tests. But the specific tool for pathway enrichment isn't named here. The GSEA (Gene Set Enrichment Analysis) is mentioned in the context of combining mitochondrial and redox categories, but the tool isn't specified. The answer might be that they used their own in-house scripts or BioMart's annotations, but the exact tool isn't clear. However, in the "Statistics" section, they mention hypergeometric tests. Wait, maybe the tool isn't explicitly stated, so the answer could be "not described."

2. **Was a tool version number provided?**
Since the previous question is about the tool, and the answer might be that the tool isn't specified, then the version number isn't provided either. But in the Statistics section, they mention R version 3.0.2, but that's for descriptive statistics, not specifically for pathway enrichment. So the answer here might be "not described."

3. **What gene set library was queried?**
The gene annotations were obtained from Vectorbase using BioMart. The functional categories like apoptosis, chemosensory response, etc., seem to be custom categories based on the authors' definitions, possibly derived from Vectorbase. However, the specific gene set library (like GO, KEGG) isn't explicitly stated here. The authors mention assigning functional groups to categories based on their own definitions, so maybe they used their own annotations. The answer might be that they used Vectorbase's annotations, but the exact library (e.g., GO) isn't specified. So maybe "not described" or "Vectorbase annotations."

4. **Was a background gene list defined for pathway enrichment analysis?**
The authors mention comparing each functional subset to the corresponding group within the set of all coding genes (n = 14,626). So yes, they used all coding genes as the background. The answer here is "yes," using all coding genes as the background.

5. **What statistical test was used for enrichment analysis?**
The statistics section says binomial probability distributions and hypergeometric tests were calculated. So the hypergeometric test was used for enrichment analysis.

6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?**
In the Methods section under the statistics part, they mention using the Benjamini-Hochberg False Discovery Rate (FDR) with alpha = 0.01. So the answer is yes, FDR correction was used.

Now, compiling all this into the answers as per the questions.
</think>

1. **What tool was used for pathway enrichment analysis?**  
   **Answer:** Not described. The text mentions functional group comparisons using hypergeometric tests but does not specify a dedicated tool (e.g., DAVID, GSEA).  

2. **Was a tool version number provided?**  
   **Answer:** Not described. The R version (3.0.2) is mentioned for descriptive statistics, but no version is noted for pathway enrichment tools.  

3. **What gene set library was queried?**  
   **Answer:** Vectorbase annotations (via BioMart) were used to assign functional categories. Specific databases like GO or KEGG are not explicitly mentioned.  

4. **Was a background gene list defined for pathway enrichment analysis?**  
   **Answer:** Yes. The background gene list was defined as all coding genes (n = 14,626).  

5. **What statistical test was used for enrichment analysis?**  
   **Answer:** Hypergeometric test.  

6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?**  
   **Answer:** Yes. The Benjamini-Hochberg False Discovery Rate (FDR, alpha = 0.01) was applied.  

---

### Collated Table:
| Question | Answer |
|----------|--------|
| 1. Tool used for pathway enrichment analysis | Not described |
| 2. Tool version number provided | Not described |
| 3. Gene set library queried | Vectorbase annotations (via BioMart) |
| 4. Background gene list defined | Yes (all coding genes, n = 14,626) |
| 5. Statistical test for enrichment | Hypergeometric test |
| 6. FDR correction used | Yes (Benjamini-Hochberg, alpha = 0.01) |