Okay, let's tackle this query step by step. The user wants me to examine how the pathway enrichment analysis was conducted in the provided scientific article. They’ve listed six specific questions to answer, and they want the answers collated into a table. First, I need to look through the article for the Methods section, but if it's not there, check other sections. The user mentioned focusing on the Methods section, but other sections might have relevant info. Looking at the article, the Methods section isn't explicitly provided in the given text. However, in the Discussion and other sections, there's mention of tools and databases. For example, in the section about the GO functional enrichment analysis, the authors mention using ToppFun, which is part of the ToppGene suite. 1. **What tool was used for pathway enrichment analysis?** The article states, "Results were obtained through ToppFun, an application of the ToppGene suite." So the tool is ToppFun. 2. **Was a tool version number provided?** The article doesn't mention a version number for ToppFun. So the answer is no. 3. **What gene set library was queried?** The GO functional enrichment analysis is mentioned, and the gene set libraries are listed as GO (Gene Ontology). Also, the miRNA targets are from hsa-miR-143, hsa-miR-223, and hsa-miR-29 families, but the gene set library for pathway enrichment would be GO. 4. **Was a background gene list defined?** The article doesn't specify a background gene list. It just mentions analyzing 82 genes, with 30 significantly deregulated. No mention of a background list. 5. **What statistical test was used?** The article doesn't specify the statistical test used for the enrichment analysis. It just mentions the results with p-values and FDR corrections. 6. **Was false discovery rate correction used?** Yes, the article mentions "false discovery rate (FDR) correction" in the results, indicating that it was applied. Now, compiling these answers into the table format as requested, making sure each question is addressed separately. For any missing information, I need to state "not described." | **Question** | **Answer** | |--------------|------------| | 1. What tool was used for pathway enrichment analysis? | ToppFun (part of the ToppGene suite) | | 2. Was a tool version number provided? | Not described | | 3. What gene set library was queried? | Gene Ontology (GO) | | 4. Was a background gene list defined for pathway enrichment analysis? | Not described | | 5. What statistical test was used for enrichment analysis? | Not described (only p-values and FDR corrections are mentioned) | | 6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis? | Yes (as indicated by "false discovery rate (FDR) correction" in the results) |