Okay, let me try to figure out the answers to these questions based on the information provided in the article. First, the user is asking about the pathway enrichment analysis conducted in the study. Let me start by recalling the relevant sections of the article. The Methods section isn't explicitly provided here, but the Abstract and Discussion mention pathway enrichment analysis. Question 1: What tool was used for pathway enrichment analysis? In the Abstract, under the "Abstract" section, it says "pathway enrichment analysis was performed on all 438 genes." The specific tool isn't mentioned in the Abstract. However, in the Discussion, under the section about miRNAs, they mention using three online databases (miRBD, TargetScan, and miRWalk) for predicting target genes, but that's for miRNA targets, not pathway analysis. The pathway analysis itself is mentioned in the context of analyzing the 438 target genes. The article doesn't specify the tool used here. So I might have to look elsewhere. Wait, in the Methods section, if it's not provided, then maybe it's in the Supplementary Material. The user mentions that the Supplementary Material is a PDF, but I can't access that. Since the user says to focus on the provided text, I'll check again. The article's "Methods" section isn't included here, but in the Discussion, when they talk about the pathway analysis, they don't specify the tool. So the answer is "not described." Question 2: Was a tool version number provided? Since the tool isn't even specified, the version number isn't provided. Answer: Not described. Question 3: What gene set library was queried? The Abstract mentions KEGG, as it says "multiple pathways, such as the insulin signalling pathway, Wnt signalling pathway, FoxO signaling pathway and mTOR signalling pathway, etc. are involved." The "etc." suggests that KEGG is the library used. Alternatively, in the Discussion, when they discuss the pathways, they list them, and KEGG is a common pathway database. However, the article doesn't explicitly state which library was used. Wait, in the Abstract, they mention "pathway enrichment analysis," and in the Discussion, they reference pathways like KEGG's. But the article doesn't state the library. However, in the context of the study, the pathways listed (insulin, Wnt, FoxO, mTOR) are all KEGG pathways. But the user is asking for what was actually used. Since the article doesn't specify, the answer is "not described." Wait, but the Abstract says "pathway enrichment analysis was performed on all 438 genes." The method isn't detailed here. However, in the Discussion, the authors mention "KEGG, Reactome or other"? The user is asking for the library. The answer is not described because the article doesn't explicitly mention the gene set library used. However, in the Abstract, they mention KEGG-like pathways (e.g., insulin signaling, Wnt, etc.), but the actual library isn't stated. So the answer is "not described." Question 4: Was a background gene list defined? The article doesn't mention defining a background gene list. They analyzed the 438 target genes, but there's no indication of a background. Answer: Not described. Question 5: What statistical test was used? The article doesn't specify the statistical test. It just says "pathway enrichment analysis was performed." So answer: Not described. Question 6: Was false discovery rate correction used? Again, the article doesn't mention any correction method for multiple testing. So answer: Not described. I need to make sure I didn't miss any details. The user mentioned to check all sections, so maybe the Methods section, but it's not provided here. The answer for each question is "not described" because the article doesn't provide the necessary details. Here is the collated answer to the questions about the pathway enrichment analysis in the article: | **Question** | **Answer** | |--------------|------------| | **1. What tool was used for pathway enrichment analysis?** | **Not described**. The article does not specify the tool used for pathway enrichment analysis. | | **2. Was a tool version number provided?** | **Not described**. No version number is mentioned. | | **3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** | **Not described**. While pathways like insulin signaling, Wnt, FoxO, and mTOR are listed, the specific library (e.g., KEGG, Reactome, GO) is not explicitly stated. | | **4. Was a background gene list defined for pathway enrichment analysis?** | **Not described**. The article does not mention the use of a background gene list. | | **5. What statistical test was used for enrichment analysis?** | **Not described**. The method of statistical testing (e.g., hypergeometric test, Fisher’s exact test) is not provided. | | **6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** | **Not described**. There is no mention of FDR correction or other methods for multiple testing. | **Notes**: - The article references pathway enrichment results (e.g., insulin signaling, Wnt) but does not detail the methodology (tools, libraries, statistical tests, or corrections). - The focus on miRNAs and their targets is addressed, but the pathway analysis itself is not elaborated. - Supplementary Material is referenced, but its contents are not accessible here. All answers are based on the provided text.