Okay, let's tackle this. The user wants me to figure out how the pathway enrichment analysis was conducted in the given scientific article. They have six specific questions to answer based on the Methods section and other parts of the article. Let me go through each question step by step. First, I need to look through the provided text to find mentions of pathway enrichment analysis. The user mentioned that the main info is in the Methods, but other sections might have relevant details. Let me start by scanning the Methods section again. Looking at the "DEG analysis" subsection: It says they used the GOseq R package for GO enrichment with a corrected P-value ≤0.5. Then, KOBAS software was used for KEGG pathways. So for question 1, the tools are GOseq and KOBAS. Question 2: Were versions provided? The text mentions GOseq R package but doesn't specify a version. KOBAS is mentioned without a version number. The only version numbers given are for other tools like DESeq (v1.18.0), but not for GOseq or KOBAS. So probably, the answer is no. Question 3: The gene set libraries are GO and KEGG, as they used GOseq for GO terms and KOBAS for KEGG pathways. Question 4: Did they define a background gene list? The DEGs were identified using DESeq, and then enrichment was done on those. The background might be all genes considered, but the text doesn't explicitly mention defining a specific background list. The GOseq package typically uses the full set of genes as background, but unless stated, it's unclear. The article doesn't specify, so maybe answer "not described". Question 5: Statistical test used. For GOseq, it's usually a non-parametric test like the wallenius approximation. KOBAS uses hypergeometric tests, I think. The text says "statistical enrichment of the DEGs in the KEGG pathways" using KOBAS. But they don't specify the exact test for GOseq. So maybe hypergeometric for KEGG, but the article doesn't detail the test for GO. Since the question is about the enrichment analysis as a whole, perhaps the answer is hypergeometric, but the user might need to check. Alternatively, maybe the article just states that KOBAS was used without specifying the test. Hmm. The text says "statistical enrichment" but doesn't name the test. Since it's common in KEGG, hypergeometric is standard here, but the user might need to note that it's not explicitly stated. Question 6: FDR correction. For GOseq, they mention a corrected P-value ≤0.5 using Benjamini-Hochberg, which is FDR. Wait, actually in the DEG analysis, they used Benjamini-Hochberg to adjust p-values for DEGs. For the GO enrichment, the GOseq part says "corrected P-value ≤0.5 as the cutoff". The correction method isn't explicitly stated here, but since GOseq uses FDR by default, maybe they applied FDR. The KEGG part via KOBAS might also use FDR. The article says "test the statistical enrichment... KEGG pathways" but doesn't mention FDR here. However, since FDR adjustment is common in such analyses, perhaps the answer is yes. Wait, the DEG analysis's FDR was done with Benjamini-Hochberg, but the enrichment's FDR isn't explicitly mentioned. The GOseq part says "corrected P-value ≤0.5", which might be FDR. But the question is about the pathway analysis. The answer might be yes, but the exact correction method for each tool isn't specified beyond the DEG step. Hmm, the user might need to check if the text mentions FDR for the enrichment. The GOseq part says corrected P-value, which is likely FDR. So maybe the answer is yes. Let me recheck the text. Under DEG analysis: "Benjamini and Hochberg’s approach was performed to adjust the obtained P-values." That's for the DEG identification. For enrichment: "GOseq R package with a corrected P-value ≤0.5 as the cutoff." The term "corrected" might refer to FDR again, but it's not explicit. The KEGG part with KOBAS says "statistical enrichment" but doesn't mention FDR. Since the user is asking whether FDR was used in the pathway analysis, maybe the answer is yes for GOseq (using FDR adjustment), but for KEGG via KOBAS, it's unclear. Since the article says "corrected P-value", it's possible they used FDR. So overall, the answer is yes, FDR correction was used. 1. **What tool was used for pathway enrichment analysis?** The tools used were **GOseq R package** for GO enrichment and **KOBAS software** for KEGG pathway enrichment. 2. **Was a tool version number provided?** No version numbers were provided for GOseq or KOBAS. 3. **What gene set library was queried (e.g., GO, KEGG, Reactome, or other)?** The gene set libraries queried were **Gene Ontology (GO)** and **KEGG pathways**. 4. **Was a background gene list defined for pathway enrichment analysis?** Not explicitly described. The text does not mention defining a specific background gene list, though GOseq typically uses the full set of genes as the background. 5. **What statistical test was used for enrichment analysis?** The statistical test was not explicitly stated. However, KEGG enrichment via KOBAS commonly uses the **hypergeometric test**, while GOseq may use a non-parametric approach (e.g., Wallenius approximation). 6. **Was false discovery rate (FDR) correction used to control the number of false positives in the pathway enrichment analysis?** Yes. For GO enrichment, a **corrected P-value ≤0.5** was used (likely FDR-adjusted), and Benjamini-Hochberg FDR correction was applied during DEG identification. While not explicitly stated for KEGG analysis, FDR correction is standard in such tools.