Okay, let's tackle this query. The user wants to know how the pathway enrichment analysis was conducted in the provided scientific article. They have six specific questions about the methods used. Since the user mentioned that the Methods section is the primary source but info could be elsewhere, I need to go through the text carefully. First, I'll look for any mention of tools used. The article mentions using GO terms in the Results section when discussing pathway analysis. For example, in the part about supplementary figures, they refer to "Supplementary Fig. 3" which is about GO terms. But the exact tool isn't named here. The Methods might have more details. Let me check the Methods section again. Wait, the user provided the whole article text, so I need to search through it. Scanning through the text, under the Results, they mention "pathway enrichment analysis" but don't specify the tool. The closest is when they refer to "GO" in the supplementary info, like Supplementary Fig. 3 is labeled "Gene Ontology (GO) terms for differentially expressed genes." However, the exact tool like DAVID, ClusterProfiler, or others isn't mentioned. Hmm, maybe it's not explicitly stated. Next, the version of the tool. Since the tool isn't named, the version probably isn't provided either. For the gene set library, they do mention GO terms and in the pathway enrichment, they refer to "pathway markers" like TGFB and BMP, which could be part of GO or KEGG. The supplementary figure 7c also talks about TGFB and BMP signaling pathways, which are KEGG pathways. But the article doesn't explicitly say if they used KEGG or just GO. The text mentions "Gene Ontology (GO)" in the supplementary figure caption, so maybe GO was the main library. But since the question allows for other like KEGG, maybe both? The user's example shows the answer might be "GO" here. Background gene list: The article doesn't specify whether a background list was defined. They might have used all genes on the array or transcriptome, but it's not stated. Statistical test: The methods might have used a hypergeometric test or Fisher's exact test common in enrichment analyses. But the article doesn't mention which test was used. The Results talk about "statistical significance" but without specifics. FDR correction: The term FDR isn't mentioned. They might have used FDR, but since it's not stated, I can't assume. The article mentions "false discovery rate correction" only in the question, but in the text, they refer to "significance" without specifying correction methods. Wait, looking at the "Supplementary information" part, the files include Supplementary Table 5 which might have details, but without access to the actual files, I can't check. The text provided here doesn't elaborate further. The main article's Methods section, which the user provided, doesn't have a detailed pathway analysis section. The Results mention pathway analysis but don't detail the methods beyond using GO terms. So, compiling the answers based on the given text: 1. Tool: Not described explicitly, but inferred to possibly use GO terms, but the tool isn't named. The answer should be "not described." 2. Version: Since the tool isn't named, version isn't provided. 3. Gene set library: They mention GO and pathways like TGFB/BMP, which are in KEGG. But the article specifically refers to GO in the supplementary figure, so maybe GO is the main one. But the question asks what was queried. The article says "Gene Ontology (GO)" so the answer is GO. 4. Background gene list: Not described. 5. Statistical test: Not described. 6. FDR correction: Not described. Wait, in the Results section under the pathway analysis part, they might have used standard methods. For example, "pathway enrichment analysis" typically uses hypergeometric test with FDR, but since it's not stated here, I have to stick to what's written. The article doesn't specify any of these details except mentioning GO terms. Therefore, the answers are mostly "not described" except for the gene set library which is GO. 1. **Tool used for pathway enrichment analysis?** Not described. The article mentions "Gene Ontology (GO)" terms in supplementary figures (e.g., Supplementary Fig. 3) but does not specify the tool (e.g., DAVID, ClusterProfiler, or others). 2. **Tool version number provided?** Not described. 3. **Gene set library queried?** Gene Ontology (GO) terms are referenced in the supplementary figures (e.g., Supplementary Fig. 3), but no other libraries like KEGG or Reactome are explicitly mentioned. 4. **Background gene list defined?** Not described. The article does not specify whether a background gene list was used for the analysis. 5. **Statistical test used?** Not described. The article does not mention the statistical test (e.g., hypergeometric test, Fisher’s exact test) applied for enrichment analysis. 6. **False discovery rate (FDR) correction used?** Not described. While the study mentions "statistical significance" in pathway analysis (e.g., Supplementary Fig. 3), there is no explicit mention of FDR or other correction methods to control false positives. --- ### Summary Table: | Question | Answer | |----------|--------| | 1. Tool used? | Not described | | 2. Tool version? | Not described | | 3. Gene set library? | GO (Gene Ontology) | | 4. Background gene list? | Not described | | 5. Statistical test? | Not described | | 6. FDR correction? | Not described |