<think>
Okay, let's look at the user's query. They want me to carefully examine how pathway enrichment analysis was conducted in the provided scientific article. The user is asking six specific questions about the methods used, and they want each question answered separately for a table. The answer should be based on the Methods section, but other sections might have relevant info too.

First, I need to go through the Methods section and find where pathway enrichment is mentioned. Let me start by skimming through the sections. The RNA-Seq part is about data processing, mapping, and DEG analysis. Then there's a section on DEG analysis. 

Looking at the DEG analysis part: "GO enrichment analysis of the DEGs was performed by the GOseq R package with a corrected P-value ≤0.5 as the cutoff. KOBAS software was used to test the statistical enrichment of the DEGs in the KEGG pathways." 

So here, the tools mentioned are GOseq for GO enrichment and KOBAS for KEGG. The user's first question is about the tool used for pathway enrichment. The answer would be both GOseq and KOBAS, but since the question is about pathway enrichment, maybe KOBAS is the main one here for KEGG. 

Question 2 asks about the tool version. The text mentions "GOseq R package" but doesn't specify a version. Similarly, "KOBAS software" is mentioned without a version number. So the answer to question 2 is no version provided for either tool.

Question 3 is about the gene set library. GOseq is for GO, and KOBAS is for KEGG pathways. So the answer includes both GO and KEGG.

Question 4 asks if a background gene list was defined. The text doesn't mention anything about a background gene list. The analysis was done on DEGs, but it's not clear if they used all genes in the genome as background or just the DEGs. So the answer is not described.

Question 5 is about the statistical test. For GOseq, it uses statistical routines, but the specific test isn't mentioned. KOBAS is used to test statistical enrichment, but again, the exact test isn't specified. So the answer is not described.

Question 6 is about FDR correction. The text says "corrected P-value ≤0.5" for GOseq, which implies some correction was done, but it doesn't specify FDR. However, in the DESeq part, they mention Benjamini and Hochberg's approach for FDR. But for the pathway analysis, it's unclear if FDR was used. The answer might be not described, but the GOseq part mentions a corrected P-value, which could be FDR. However, the exact method isn't specified. The user's question is about FDR correction specifically. Since the text doesn't explicitly state FDR was used for the pathway analysis, the answer is not described.

So putting it all together:

1. Tools: GOseq and KOBAS.
2. Version: Not provided.
3. Libraries: GO and KEGG.
4. Background: Not described.
5. Statistical test: Not described.
6. FDR correction: Not described.

I need to make sure I didn't miss any other sections. The Results might mention some pathways but not the methods. The Additional files mention phenylopropanoid pathways, but that's about the results, not the methods. The Acknowledgements don't mention methods. So the answer should be based strictly on the Methods section.
</think>

Here is the collated answer to your questions based on the **Methods section** of the article:

| **Question**                                                                 | **Answer**                                                                 |
|-----------------------------------------------------------------------------|----------------------------------------------------------------------------|
| **1. What tool was used for pathway enrichment analysis?**                  | **GOseq R package** (for GO enrichment) and **KOBAS software** (for KEGG pathway enrichment). |
| **2. Was a tool version number provided?**                                  | **No**. The article does not specify version numbers for GOseq or KOBAS. |
| **3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** | **GO** (Gene Ontology) and **KEGG** (Kyoto Encyclopedia of Genes and Genomes) pathways. |
| **4. Was a background gene list defined for pathway enrichment analysis?**  | **Not described**. The article does not explicitly mention defining a background gene list (e.g., all genes in the genome or DEGs). |
| **5. What statistical test was used for enrichment analysis?**              | **Not described**. The article mentions "statistical enrichment" but does not specify the exact statistical test (e.g., hypergeometric, Fisher’s exact test). |
| **6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** | **Not described**. The article does not explicitly state whether FDR correction (e.g., Benjamini-Hochberg) was applied to the pathway enrichment results. |

---

### Key Notes from the Article:
- **GO enrichment** was performed using the **GOseq R package** with a corrected *P*-value ≤ 0.5 as the cutoff, but the correction method is unspecified.  
- **KEGG pathway enrichment** was analyzed using **KOBAS software**, but no details about statistical tests or corrections are provided.  
- The article does not clarify whether the background gene set (e.g., all annotated genes in *G. hirsutum*) was used for enrichment analysis.  
- While **FDR correction** is mentioned in the context of differential gene expression analysis (DESeq), this is not explicitly extended to pathway enrichment analysis.  

If further details are required, the **Additional files** (e.g., Additional file 3) may provide supplementary pathway-related data but not methodological specifics.