Thinking... We need to answer 6 questions about pathway enrichment analysis. Provide table with columns: Tool used, Tool version(s) described, Gene set libraries used, Custom background used? (Yes/No/Not described), Statistical test(s) used, Multiple testing correction? Yes/No. We need to extract only explicitly reported details. Let's read relevant sections. From Methods: "Target prediction and enrichment analysis" section. The article says: "To investigate the mechanisms underlying miR-148b-3p, miR-190b, and miR-429 functions, 9 online databases were scanned to predict target genes. We gathered target genes predicted by at least 4 algorithms to obtain 405 target genes for miR-148b-3p, 76 target genes for miR-190b, and 299 target genes for miR-429 ([100]Supplementary Table 2). These genes were subjected to GO and pathway enrichment analyses ([101]Supplementary Tables 3, [102]4, [103]5). The result revealed that the targets of candidate miRNAs were involved in several critical cancer-related pathways, including transforming growth factor (TGF)-beta signaling pathway, Wnt signaling pathway, p53 pathway, p38 mitogen-activated protein kinase (MAPK) pathway and mammalian target of rapamycin (mTOR) signaling pathway ([104]Figure 6)." It does not explicitly name the enrichment tool used. It says "pathway enrichment analyses". No tool name like DAVID, GSEA, etc. So tool not described. So we must say "Not described". Were enrichment tool versions described? Not described. Which gene set libraries used? The article mentions GO and pathway enrichment analysis. It says "The result revealed that the targets of candidate miRNAs were involved in several critical cancer-related pathways, including transforming growth factor (TGF)-beta signaling pathway, Wnt signaling pathway, p53 pathway, p38 mitogen-activated protein kinase (MAPK) pathway and mammalian target of rapamycin (mTOR) signaling pathway ([104]Figure 6)." This refers to "pathways" but not specify which database library used (e.g., KEGG, Reactome). It does not mention GO explicitly, though the supplementary tables maybe have GO functional annotation. In Methods, earlier there is no mention of gene set libraries or database. The article just says "GO and pathway enrichment analyses" but not specify which library or database. But in supplementary materials, there are "Supplementary Table 3 GO functional annotation and pathway analyses of has-miR-148b-3p" etc. So maybe they used GO annotations and KEGG or others. But the article does not explicitly mention which libraries used. It says "GO and pathway enrichment analyses" but not the library names. Wait in Methods: "The result revealed that the targets of candidate miRNAs were involved in several critical cancer-related pathways, including transforming growth factor (TGF)-beta signaling pathway, Wnt signaling pathway, p53 pathway, p38 mitogen-activated protein kinase (MAPK) pathway and mammalian target of rapamycin (mTOR) signaling pathway ([104]Figure 6)." So they mention these pathways but not the source database. So gene set libraries used are not described. But maybe in Supplementary Tables, they refer to GO functional annotation and pathway analyses. For example, Supplementary Table 3 "GO functional annotation and pathway analyses of has-miR-148b-3p" etc. So they used GO annotations. They might have used GO database. But the article does not explicitly mention the library used. The article might mention "GO" but not explicitly. Wait, the article says: "These genes were subjected to GO and pathway enrichment analyses ([101]Supplementary Tables 3, [102]4, [103]5)." This line indicates they performed GO and pathway enrichment analyses. The phrase "GO and pathway enrichment analyses" suggests GO and some pathway database. But they didn't specify which database. But it might be implied that GO is a gene set library. The article says "GO functional annotation and pathway analyses" but no database names. But we need to answer the questions as explicitly described. So question 1: What tool was used for pathway enrichment analysis? The article does not mention any tool. So answer: Not described. But wait: The article mentions "These genes were subjected to GO and pathway enrichment analyses". They didn't say which tool. So "Not described". Second question: Were enrichment tool version(s) described? Not described. Third: Which gene set libraries were used? They mention GO and pathways. But they did not specify a particular database like KEGG. They just mention GO functional annotation and pathway analyses. In Supplementary Table 3, 4, 5: they refer to GO functional annotation and pathway analyses. So gene set libraries: GO. They also mention "pathway analyses" but no specific library. So maybe only GO. But the article states "GO functional annotation and pathway analyses". It didn't specify which database for pathways. So we can list "GO" as a gene set library. Possibly "KEGG" is not mentioned. So we list "GO". Fourth: custom background gene list? Options: Yes, No, Not described. The article does not mention using a custom background gene list. So "Not described". Fifth: What statistical test(s) were used in enrichment analysis? Not described. Sixth: Was multiple testing correction / FDR applied to enrichment analysis? Not described. But we need to provide output in table format. Each row maybe for each question? Wait, the instructions: Provide output in table format. Likely each column for each question and answer. Or each row for each tool. But we need to output table with columns: "Tool used", "Enrichment tool versions", "Gene set libraries", "Custom background used", "Statistical tests used", "Multiple testing correction applied". Better to produce a single row summarizing all, but if more than one tool used, we list each separately. But here we only have "Not described" for all. However, the instruction: "If more than one tool, method, or database is used, list all of them separately." For each column, we list all. For each row maybe we list separate tools? But it's not specified. Provide output in table format. So maybe each row for each tool, but if no tool, row with "Not described"? But we must answer the 6 questions. The output can be a table with column names and values for each question. Thus: | Question | Answer | |----------|--------| | Tool used for pathway enrichment analysis | Not described | | Enrichment tool versions | Not described | | Gene set libraries used | Not described | | Custom background gene list used | Not described | | Statistical tests used | Not described | | Multiple testing correction applied | Not described | But we must follow format: table with 6 columns maybe? The instruction: "Provide output in table format." So likely produce a table with each question as row and answer as column. The question numbers maybe: "What tool was used for pathway enrichment analysis?", etc. So table columns: Question #, Question text, Answer. But we just provide a table with 6 rows and 2 columns: "Question" and "Answer". But the instructions: "If more than one tool, method, or database is used, list all of them separately." So if tool used, list all. But we have "Not described". Let's produce a table with columns: "Category", "Details". Categories: Tool, Tool versions, Gene set libraries, Custom background, Statistical tests, Multiple testing correction. Thus table: | Category | Details | |----------|---------| | Tool used for pathway enrichment analysis | Not described | | Enrichment tool versions | Not described | | Gene set libraries used | Not described | | Custom background gene list used | Not described | | Statistical test(s) used | Not described | | Multiple testing correction applied | Not described | But the instructions say: "If more than one tool, method, or database is used, list all of them separately." That means if there were multiple tools, we would list each in a separate line under that column. But we have only one row. Let's produce final answer accordingly. ...done thinking. | **Category** | **Details** | |--------------|-------------| | Tool used for pathway enrichment analysis | Not described | | Enrichment tool version(s) | Not described | | Gene set libraries used | Not described | | Custom or specific background gene list used | Not described | | Statistical test(s) used | Not described | | Multiple testing correction / FDR applied | Not described |