Okay, I need to figure out how the pathway enrichment analysis was conducted in this article. Let me start by looking through the provided text. The user mentioned that the Methods section might have the details, but other sections could also have relevant info. First, the question is about the tool used for pathway enrichment. The article mentions "pathway enrichment analysis" in the Results section. It says they used three online miRNA-target-predicting databases: miRBD, TargetScan, and miRWalk. Then, after getting the target genes, they performed pathway enrichment analysis. The results indicated involvement in pathways like insulin signaling, Wnt, FoxO, and mTOR. Wait, but the exact tool for the enrichment isn't named here. Let me check again. The Methods section isn't fully provided here, but the user included the abstract and some sections. The part under the Results says they did the analysis after getting the target genes. The Supplementary Material might have more details, but since it's not accessible here, I have to go with what's given. Hmm, maybe in the Methods, when they talk about the analysis of differentially expressed miRNAs, they might mention the tool. The user's provided text includes a section where they mention using three databases for target prediction, then pathway analysis. The Results state that the target genes were analyzed for pathway enrichment, but the specific tool isn't named. The term "pathway enrichment analysis" is used without specifying the software, like DAVID, GOstats, clusterProfiler, or KEGG itself. Looking at the question 1 again: the tool used. Since the article mentions KEGG pathways (like insulin signaling, Wnt, etc.), perhaps they used KEGG's own tools or a common tool like DAVID or clusterProfiler in R. But since the article doesn't explicitly name the tool, maybe it's not described. Wait, in the first part, the user's text says "pathway enrichment analysis was performed on all 438 genes." The Methods might not have been detailed here. The user's provided text under the problem includes the Methods section? Let me check again. Looking back at the user's input: the user pasted the entire article's sections, including the Methods? Wait, the user provided the abstract and then sections like Acknowledgments, but in the middle, under the Results, they talk about pathway analysis. The user's input includes a section titled "Supplementary Material" but no explicit Methods section. Wait, actually, the user's input includes the Methods? Let me check again. Looking again, the user's input starts with the abstract, then the main text which includes sections like Results and Discussion, but the Methods might not be fully present. The user mentions that the Methods section should be checked, but in the provided text, maybe the Methods section is missing? Wait, the user says "Carefully examine how pathway enrichment analysis was conducted in this scientific article. Focus on the Methods section, but information can also be found in other sections." But in the provided text, the Methods section might not be included here. Wait, looking at the text provided by the user, after the abstract, it seems to go into the main body, perhaps skipping the Methods. The user included the Results and Discussion parts where they mention pathway analysis but not the Methods. Wait, the user's input includes a section starting with "Supplementary Material" but the actual Methods might have been part of the main text. Let me check again. In the user's input, under the Results section, they mention: "To further understand the role of these up-regulated miRNAs, pathway enrichment analysis was performed on all 438 genes." The authors then list the pathways like insulin, Wnt, etc. But they don't mention the tool. Wait, maybe in the Methods? Let me check again. The user's input includes a section titled "Supplementary Material" but perhaps the Methods are in the main text. The user's text after the abstract includes sections like "HIF-1α/Rab22 pathway mediates EV production during HPC", then "HPC EVs protect renal I/R injury in vivo", then "Differential EV-miRNAs in HPC EVs versus normoxic EVs", then "Pathway analysis of target genes of differential EV-miRNAs". In this last section, they might mention the methods. Let me check that part again. The user's provided text under "Pathway analysis of target genes of differential EV-miRNAs" says: "To deepen the understanding... we utilized three online miRNA-target-predicting database (miRBD, TargetScan and miRWalk) to predict the target genes. Target genes located in the intersection of three databases were chosen for further analyses so that to reduce false positives. Results showed these up-regulated EV-miRNAs were associated with 438 target genes. To further understand the role of these up-regulated miRNAs, pathway enrichment analysis was performed on all 438 genes." Then they list the pathways. But no tool is mentioned here. Hmm. Since the authors mention KEGG pathways (e.g., insulin signaling, Wnt, FoxO, mTOR), perhaps they used KEGG's own pathway analysis tool, but that's an assumption. Alternatively, they might have used DAVID or another common tool. But since the article doesn't specify the tool, the answer would be "not described". The same applies to the other questions. Let me check each question again. 1. Tool: Not described. The article mentions pathway enrichment but doesn't name the tool. 2. Tool version: Not described because the tool isn't named. 3. Gene set library: They mention KEGG pathways, so likely KEGG. Since the pathways listed are KEGG pathways (like insulin signaling is a KEGG pathway). So the library is KEGG. 4. Background gene list: The article doesn't mention defining a background list. They used the 438 target genes as the input, so perhaps the background is the entire genome or the target genes? Not clear. Since it's not specified, answer is "not described". 5. Statistical test: They don't mention which statistical test (e.g., hypergeometric, Fisher's exact). Not described. 6. FDR correction: The article mentions "pathway enrichment analysis was performed", but doesn't specify if FDR was used. The term "false discovery rate" isn't mentioned here. So answer is "not described". Wait, but in some cases, tools like DAVID automatically apply FDR. However, without explicit mention, it's safer to say not described. So compiling the answers based on the provided text: 1. Tool: Not described. 2. Tool version: Not described. 3. Gene set library: KEGG (since the pathways listed are KEGG pathways). 4. Background gene list: Not described. 5. Statistical test: Not described. 6. FDR correction: Not described. 1. **Tool**: Not described. 2. **Tool version**: Not described. 3. **Gene set library**: KEGG (implied by the listed pathways like insulin signaling, Wnt, FoxO, and mTOR). 4. **Background gene list**: Not described. 5. **Statistical test**: Not described. 6. **FDR correction**: Not described. **Summary Table**: | Question | Answer | |----------|--------| | 1. Tool used for pathway enrichment analysis? | Not described. | | 2. Tool version number provided? | Not described. | | 3. Gene set library queried? | KEGG (implied by pathways listed). | | 4. Background gene list defined? | Not described. | | 5. Statistical test used? | Not described. | | 6. FDR correction used? | Not described. |