Okay, let me try to work through this step by step. The user wants to know how the pathway enrichment analysis was conducted in the provided scientific article. They have specific questions about the tool used, version number, gene set library, background gene list, statistical test, and whether FDR correction was applied. First, I need to look through the text provided. The article's abstract and sections mention pathway enrichment, but I need to find details in the Methods section. Wait, the user mentioned that the Methods section might not be fully here, but information can be found elsewhere. Let me check the given text again. Looking through the provided sections: the abstract, introduction, results (maybe), discussion, conclusions, and additional files. The Methods section isn't explicitly present here. However, sometimes information about enrichment analysis can be found in the Results or the supplementary materials. Let me look in the Results section first. In the Results section, the authors mention that they performed pathway enrichment analysis. For example, in the part discussing metabolic balance, they refer to "meta-analysis of data retrieved from NCBI GEO database" but that might be differential expression, not enrichment. Looking at the Additional files, like Additional file 3's figure S2, which is about metabolic balance between HCC and normal tissues. The caption mentions "expression Z-score values of catabolic and anabolic enzymes" from meta-analysis. But again, not enrichment details. The main text's discussion refers to "inhibited metabolic processes and the aberrant cell cycle progression in HCC" but doesn't detail the methods. Wait, in the Conclusions, they mention "simultaneous reversal of hyper-methylation..." but that's more about their findings than methods. Hmm, maybe the Methods section is in the Additional files? The user provided links to additional files like Additional file 1 (flowchart for the network), but without access to those PDFs, I can only go by the text provided here. Looking back at the text given, the authors mention "functional annotation and correlation analyses" in the authors' contributions (KRZ did that). Maybe in the methods, they used tools like DAVID, GO, KEGG, or Reactome. The pathway terms mentioned, like cell cycle, amino acid metabolism, etc., are common in these databases. The abstract mentions "pathway enrichment analysis" but doesn't specify the tool. The results section refers to "GSEA" (Gene Set Enrichment Analysis) in the figure legends? Let me check the figures. The user mentioned "Figure S4" in Additional file 8, but without seeing it, I can't confirm. Wait, in the main text, when they talk about Figure S2 (Additional file 3), they refer to metabolic balance, but not enrichment. Wait, in the main text under the Results, they mention "pathway enrichment analysis" in the context of meth-GS and mRNA-GS scores, but not the method. Alternatively, maybe in the supplementary tables. For example, Additional file 2 lists tumor suppressors and oncogenes with hazard ratios, which might be from survival analysis, not enrichment. Alternatively, the authors might have used DAVID for enrichment. In many studies, DAVID is a common tool unless specified otherwise. The term "Gene Set Enrichment Analysis" (GSEA) is another possibility, but the user's first question is about the tool used. The article might have used GSEA, but it's not explicitly stated here. Looking again at the main text's Results section: the authors mention "pathway enrichment analysis" when discussing metabolic processes and cell cycle. For example, "suppressed metabolic signaling" and "hyperactive cell cycle signaling". The authors also refer to "existing literature" in the discussion, but not their own methods. Wait, in the "Additional files" section, the user provided links to supplementary materials, but the text here might have mentions. Let me check the "Additional files" descriptions: Additional file 3: Figure S2's caption mentions "metabolic balance" using Z-scores from GEO data. Not enrichment. Additional file 7 and 8 are about scores related to methylation and mRNA-GS. Not enrichment details. Hmm, perhaps the Methods section is not fully present here, so the user might have to infer from the text. Alternatively, maybe the tool is mentioned in the main text. Let me re-read the entire provided text again carefully. The user's provided text includes the Abstract, Introduction, Results (parts), Discussion, Conclusions, and the Additional files descriptions. In the Methods section (if present here?), but I don't see it. 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 text provided, the Methods section isn't included. Wait, looking at the Authors’ contributions, it says "KRZ downloaded the data and did functional annotation and correlation analyses..." So functional annotation (like GO/KEGG terms) was part of their methods. Maybe they used DAVID or another tool for that. The Discussion section mentions "pathway enrichment analysis" but doesn't specify. For example, when they talk about "inhibited metabolic processes and the aberrant cell cycle progression", they might have used KEGG pathways. Alternatively, since they mention "Gene Set Enrichment Analysis (GSEA)" in the figure legends (if present in the supplementary figures). For instance, Figure S4 might have used GSEA. But without seeing the actual figure captions, I can't be sure. Alternatively, the term "pathway enrichment analysis" is sometimes done with tools like GOseq, clusterProfiler in R, or using online tools like Enrichr. Since the user needs to fill in a table with the answers, and if the information isn't present in the given text, then the answer is "not described". Looking again, the key points: 1. What tool was used? The text doesn't explicitly mention the tool. They might refer to GSEA, but it's not stated. The closest is "functional annotation" which could be DAVID, but not sure. 2. Version number: Not mentioned. 3. Gene set library: They mention GO terms (since they talk about metabolic processes and cell cycle, which are GO categories) or KEGG pathways. But the text doesn't specify. 4. Background gene list: Not discussed here. 5. Statistical test: The authors might have used Fisher's exact test (common in GO enrichment) or a different test like chi-square. Not stated. 6. FDR correction: They might have used FDR (Benjamini-Hochberg), but not mentioned. Since none of these are clearly stated in the provided text, the answers are mostly "not described". 1. **Tool used for pathway enrichment analysis**: Not explicitly described. The text mentions "functional annotation" and "pathway enrichment analysis" but does not specify the tool (e.g., DAVID, GSEA, clusterProfiler). 2. **Tool version number**: Not provided. 3. **Gene set library queried**: Not explicitly stated. The analysis likely involved libraries like GO (Gene Ontology) or KEGG (Kyoto Encyclopedia of Genes and Genomes) based on context (e.g., metabolic processes and cell cycle terms), but this is inferred. 4. **Background gene list defined**: Not described. The text does not mention whether a background gene list was used. 5. **Statistical test used**: Not specified. Common tests like Fisher's exact test or hypergeometric test are typically used for enrichment but were not mentioned. 6. **False discovery rate (FDR) correction**: Not explicitly addressed. While FDR correction (e.g., Benjamini-Hochberg) is standard, the authors did not mention it in the provided text. **Summary Table**: | Question | Answer | |--------------------------------------------------------------------------|---------------------------------| | 1. Tool used for pathway enrichment analysis | Not described | | 2. Tool version number | Not described | | 3. Gene set library queried (e.g., GO, KEGG) | Not explicitly stated | | 4. Background gene list defined | Not described | | 5. Statistical test used for enrichment | Not specified | | 6. FDR correction used to control false positives | Not described |