Okay, let me tackle this step by step. The user wants to know how the pathway enrichment analysis was conducted in the provided article. They have six specific questions to answer. I need to go through the article carefully to find the relevant information. First, looking at the Methods section. Hmm, the user mentioned that the Methods might have the details, but also other sections. Since I can't see the actual Methods section here, I have to rely on the text provided. Let me scan through the given content again. The article mentions "GO and KEGG pathway analyses were performed..." in the Results or Discussion sections. For example, in the Results part, they talk about GO term analysis and KEGG pathway analysis. The tool used might be mentioned there. Looking at the Results section, they state: "GO and KEGG pathway analyses were performed to better understand the biological function..." but it doesn't specify the exact tool. However, in the Conclusions, they mention "bioinformatics analysis revealed..." which might imply common tools like DAVID, ClusterProfiler, or something else. Wait, in the Supplementary Material section, sometimes tools are mentioned. But the user hasn't provided the supplementary info. Wait, in the text provided, under the Results section, they say "The GO term analysis showed..." and "KEGG pathway analysis revealed..." but the specific tool isn't named. However, in the Discussion, they refer to "bioinformatics analysis" but again no tool name. Maybe the authors used a standard tool like DAVID or Enrichr. Alternatively, in the Conclusions they mention "constructed miRNA–mRNA regulatory networks" which might involve tools like Cytoscape, but that's for network visualization. Wait, the problem is that the actual Methods section isn't provided here. The user's given text includes the abstract, results, discussion, etc., but perhaps not the Methods. Since I can't see the Methods, I have to infer from what's here. Alternatively, perhaps in the Results they mention the tool. Let me check again. Looking at the text provided: The Results section says: "GO and KEGG pathway analyses were performed..." but no tool. The Discussion mentions "bioinformatics analysis" but again no tool. The only possible clue is in the Electronic supplementary material where Supplementary Figure 1 and 2 are mentioned, but that's about MRI and t-SNE. Wait, the authors might have used standard tools like DAVID (Database for Annotation, Visualization, and Integrated Discovery) or ClusterProfiler in R. Since they mention KEGG and GO, which are common in such tools. Since the article is about pathway analysis, maybe they used DAVID or another common tool. But the article doesn't specify the exact tool. Since the question asks what tool was used, but the article doesn't state it, then the answer would be "not described". Next question: tool version. If the tool isn't mentioned, version isn't provided either, so "not described". For the gene set library: They used GO and KEGG, as stated in the Results. So the answer is "GO and KEGG". Background gene list: The article doesn't mention whether they used a specific background list. The question is whether they defined a background list (like all genes on the array). Since they are analyzing co-differentially expressed genes, maybe the background is all genes tested. But the article doesn't specify, so "not described". Statistical test: The article mentions "enrichment analysis" but doesn't specify the test. Common tests are hypergeometric or Fisher's exact test for GO/KEGG. But without explicit mention, it's "not described". FDR correction: They mention "false discovery rate correction" in the context of some analysis? Let me check. In the Results, they talk about "significantly enriched" but didn't mention FDR. However, in the Methods (if present) they might have used FDR. Since the article provided doesn't mention, the answer is "not described". Wait, but looking again in the text: The user's provided text says "KEGG pathway analysis revealed that the co-differentially expressed DEmRNAs were significantly enriched..." The term "significantly" might imply that they used some multiple testing correction, but it's not explicitly stated. Since the question is whether FDR was used, and the article doesn't say, then it's "not described". So compiling all answers: 1. Tool: Not described (since they just mention GO and KEGG but not the tool) 2. Version: Not described 3. Gene sets: GO and KEGG 4. Background gene list: Not described 5. Statistical test: Not described 6. FDR correction: Not described Wait, but maybe in the pathway analysis, they did use a standard approach where FDR is typically applied. But since the article doesn't mention it, we have to go with what's written. The user instructions say if authors didn't provide details, write "not described". 1. **What tool was used for pathway enrichment analysis?** Not described. The article mentions performing GO and KEGG pathway analyses but does not specify the exact tool (e.g., DAVID, ClusterProfiler, or others). 2. **Was a tool version number provided?** Not described. 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) were used. 4. **Was a background gene list defined for pathway enrichment analysis?** Not described. The article does not mention whether a specific background gene list was used (e.g., all genes on a microarray or transcriptome dataset). 5. **What statistical test was used for enrichment analysis?** Not described. Common tests (e.g., hypergeometric, Fisher’s exact test) are typically used for GO/KEGG enrichment, but the article does not specify the test. 6. **Was false discovery rate (FDR) correction used to control the number of false positives in the pathway enrichment analysis?** Not described. The article mentions "significantly enriched" pathways but does not explicitly address FDR correction (e.g., Benjamini-Hochberg method).