Okay, let me try to figure out the answers to these questions about the pathway enrichment analysis in the given article. The user wants me to focus on the Methods section and other relevant parts. First, the question is asking what tool was used. I remember that in some parts of the article, they mentioned using Gene Expression Omnibus (GEO) for data deposition, but that's not the analysis tool. They might have used tools like DAVID, GSEA, or something else. Let me check the Methods section again. Wait, in the "Deposition of transcriptome data" section, they mention GEO, but that's just where they stored the data. The actual analysis tools aren't specified there. Let me look through the Results and Discussion again. There's mention of gene set enrichment, like the 19-gene cohort of pluripotency markers. However, the specific tool isn't named here. The authors might not have provided the tool details, so the answer might be "not described." Next, the version number. If the tool isn't specified, then the version number is also not described. For the gene set library, they mentioned GO terms in the results. For example, they talk about downregulation of genes in pathways like TGFB and BMP. GO is likely the library used, but the article doesn't explicitly state it. So maybe "GO" is the answer, but I need to confirm. The Methods section might have mentioned it. Let me check again. The Methods section isn't detailed here, but in the results, they refer to "gene markers representing these two pathways" which might imply they used pathway databases. However, the exact library isn't specified. Since they used terms like "GO" in the context of gene markers, maybe GO is the answer. But if the article doesn't specify, the answer is "not described." Background gene list: The question is whether they defined a background. In pathway analysis, the background is usually all expressed genes or a specific set. The article doesn't mention a specific background, so the answer is likely "not described." Statistical test: They might have used a hypergeometric test or Fisher's exact test. The article mentions terms like "downregulation" and "upregulation" but doesn't specify the statistical test. So again, "not described." False discovery rate correction: The article doesn't mention any correction methods for multiple testing. They might not have used it. So answer is "not described." Putting this all together, the answers would be that the tool, version, gene set library, background, statistical test, and FDR correction are all not described unless there's some implied information. But since the user says to check the Methods section and other sections, and I don't see explicit mentions, the answers are all "not described." | **Question** | **Answer** | |--------------|------------| | 1. What tool was used for pathway enrichment analysis? | **Not described** | | 2. Was a tool version number provided? | **Not described** | | 3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)? | **Not described** | | 4. Was a background gene list defined for pathway enrichment analysis? | **Not described** | | 5. What statistical test was used for enrichment analysis? | **Not described** | | 6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis? | **Not described** | **Notes:** - The article does not explicitly describe the tools, libraries, or statistical methods used for pathway enrichment analysis in the Methods section or elsewhere. - While the text mentions gene markers and pathways (e.g., TGFB, BMP, pluripotency genes), it does not clarify the computational tools, version numbers, or statistical frameworks employed for enrichment analysis. - Deposition of data in GEO (GSE126150) is noted, but this pertains to data storage, not the analysis methodology.