Okay, let's tackle this step by step. The user wants to know how the pathway enrichment analysis was conducted in the provided article. I need to go through the text carefully to find the answers to the six questions listed. First, the article mentions that they used 9 online databases to predict target genes for the miRNAs. The target genes predicted by at least 4 algorithms were chosen. Then, they performed GO and pathway enrichment analyses. 1. **Tool used for pathway enrichment analysis**: The text says they did GO functional annotation and pathway analyses. Common tools for this include DAVID, GOplot, or ClusterProfiler. However, the exact tool isn't named here. The supplementary tables (like Supplementary Table 3-5) might have more details, but since I can't access those, I have to rely on the main text. The authors mention "GO functional annotation and pathway analyses" but don't specify the tool. So maybe it's not described. 2. **Tool version number**: Since the tool isn't specified, the version probably isn't mentioned either. 3. **Gene set library**: The article clearly states they used GO (Gene Ontology) and pathway analyses. The pathways mentioned include TGF-beta, Wnt, p53, p38 MAPK, and mTOR. These are part of GO and possibly KEGG. But the exact library isn't specified beyond GO and general pathways. The question asks for the library like GO, KEGG, etc. Since GO is mentioned, and pathways like KEGG are common, but without explicit mention of KEGG, maybe just GO and other pathway databases? The text just says "pathway" so maybe it's not fully specified. 4. **Background gene list**: The authors used target genes predicted by at least 4 algorithms. So the background might be all genes in the target databases, but it's not explicitly stated if they used a specific background list like all human genes or something else. The text doesn't mention defining a background list. 5. **Statistical test**: The article doesn't specify which statistical test was used. Enrichment tests often use hypergeometric or Fisher's exact test, but without explicit mention, this isn't described. 6. **FDR correction**: They mention controlling false positives but don't specify if FDR (like Benjamini-Hochberg) was used. The text just says "false discovery rate correction" but maybe in the context? Wait, the user's question says "was false discovery rate correction used". The article states "pathway enrichment analyses such as TGF-beta...", but the methods don't mention FDR. The answer might be not described. Wait, looking again at the Methods section (the user said to focus on Methods but info elsewhere too). The exact Methods section isn't provided here. The user's provided text includes the Abstract, Introduction, Results, Discussion, etc., but the Methods section might not be fully here. Let me recheck the given text. Looking through the provided article text, under the Results section, it says: "To investigate the underlying mechanisms... we used 9 online databases and predicted the target genes. Only the target genes predicted by at least 4 algorithms were chosen and subsequently used for GO and pathway enrichment analyses to explore the potential effects." Then in the Supplementary Materials, tables 3-5 are GO functional annotation and pathway analyses. The actual methods for the enrichment might be in the Materials and Methods, which isn't pasted here. Since the user's provided text includes the entire article except perhaps the Methods section? Wait, actually the user provided the entire article's text except maybe the Methods section? Wait, the user's input includes sections like Abstract, Introduction, Results, Discussion, Footnotes, etc., but maybe the Methods section is missing. Hmm, 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 given text, the Methods section might not be present. The user included the Results where they mention "GO and pathway enrichment analyses" but not the exact tools. So, given the information provided, the answers must be based on what's here. So, to restate: 1. Tool: Not explicitly named. They mention GO and pathway analyses, but the tool (like DAVID, Panther, etc.) isn't stated. 2. Version: No, since tool isn't specified. 3. Gene set library: GO and unspecified pathways (like KEGG might be part of it, but since they mention pathways such as TGF-beta, which could be from KEGG or other sources). The exact library (e.g., GO Biological Process, KEGG) isn't specified beyond "GO functional annotation and pathway analyses". 4. Background gene list: Not described. They used the target genes from the miRNAs that were predicted by 4+ algorithms, but the background for the enrichment (like all genes in the database) isn't mentioned. 5. Statistical test: Not specified. Common ones are hypergeometric, but not stated here. 6. FDR: The text doesn't mention FDR correction, only that they did enrichment analyses. So not described. Wait, in the results, they just report the pathways and say the analyses were done, but the methods for how (stats, FDR) aren't given in the provided text. So all answers are "not described" except maybe for the gene set libraries (GO and pathways, but exact libraries beyond GO aren't clear). Alternatively, the question 3 asks for the gene set library, like GO, KEGG, etc. The article does mention "GO functional annotation and pathway analyses", so GO is one, and "pathway" could be KEGG, Reactome, etc. But since they don't specify which pathway database, it's not fully described. So the answer for question 3 is "GO and unspecified pathway databases" but the user wants the specific library names. Since they don't specify beyond "pathway", perhaps it's considered as "not described" except that GO was used. Hmm. Alternatively, maybe the authors used a combination like GO and KEGG. Since the pathways listed (TGF-beta, Wnt, etc.) are common in KEGG, but without explicit mention, it's not certain. So, consolidating: 1. Tool: Not described (since they mention doing it but not the tool) 2. Version: Not described 3. Gene set library: GO and unspecified pathway databases. Since the user's question allows for examples like GO, KEGG, etc., but since the article says "pathway" without naming the library, maybe it's partially described as GO and pathways, but not exact libraries beyond GO. Wait, the supplementary tables are listed as "GO functional annotation and pathway analyses of has-miR-148b-3p" (Supplementary Table 3). So maybe the pathway analysis is separate from GO, but the exact pathway database isn't named. So the gene set libraries used were GO and some pathway databases (like KEGG, but not stated). Alternatively, maybe the pathway analysis is part of GO. But GO has biological processes, molecular functions, cellular components. Pathways like TGF-beta are part of BP. So maybe all under GO? But the authors mention "pathway" separately. So perhaps they used both GO and KEGG. However, since it's not specified in the text provided, I can't confirm. So, to answer the questions strictly based on the given text: 1. Tool: Not described (they mention they did it but didn't name the tool) 2. Version: Not applicable, since tool isn't named. 3. Gene set library: GO and unspecified pathway databases. Since the user asks for the library queried, like GO, KEGG, etc., and the text mentions GO and "pathway", but not the exact pathway database, it's partially described but not fully. So perhaps the answer is "GO and pathway databases (specific libraries not specified)". But the user might expect to list the libraries mentioned. Since GO is explicitly mentioned, and pathway is mentioned but not the specific library (like KEGG), so the answer is "GO and unspecified pathway databases". But the question says "gene set library", so maybe the answer is "GO and KEGG" but since it's not stated, better to say not described except for GO. Alternatively, since the pathways like TGF-beta are part of KEGG, but without explicit mention, perhaps the answer is that the gene set library is not fully described beyond GO. Hmm, this is a bit ambiguous, but given the text, I have to go with what's written. The article states they used "GO functional annotation and pathway analyses". So the gene set libraries are GO and some pathway databases (but which ones aren't specified). So for question 3, the answer is "GO and pathway databases (specific libraries not specified)". But the user wants the answer in a table, so maybe just "GO and pathways" but not specific. Alternatively, if the question requires specific names like KEGG, then it's not described beyond GO. Alternatively, perhaps the authors used a tool that combines multiple libraries, but since it's not stated, the answer is that the specific gene set libraries beyond GO are not described. For the other questions: 4. Background gene list: Not described. They mention using target genes from at least 4 algorithms but don't mention the background. 5. Statistical test: Not described. 6. FDR: Not described. So, compiling all answers accordingly. 1. **Tool used for pathway enrichment analysis**: Not described. The article mentions conducting GO and pathway enrichment analyses but does not specify the exact tool (e.g., DAVID, ClusterProfiler, or others). 2. **Tool version number**: Not described. Since the tool is not named, its version is also unspecified. 3. **Gene set library**: The analysis used Gene Ontology (GO) and unspecified pathway databases (e.g., pathways like TGF-beta, Wnt, etc., were mentioned, but the exact library like KEGG or Reactome was not explicitly stated). 4. **Background gene list**: Not described. The analysis focused on target genes predicted by at least 4 algorithms, but the broader background gene list (e.g., all human genes) was not specified. 5. **Statistical test**: Not described. Common tests like hypergeometric or Fisher’s exact test are typically used for enrichment, but the article does not mention which was applied. 6. **FDR correction**: Not described. While controlling false positives is implied, the article does not explicitly state whether FDR (e.g., Benjamini-Hochberg) was used. --- ### Summary Table: | Question | Answer | |--------------------------------------------------------------------------|-------------------------------------------------------------------------| | 1. Tool used for pathway enrichment analysis | Not described. Mentioned GO and pathway analyses but no specific tool. | | 2. Tool version number | Not described. | | 3. Gene set library (e.g., GO, KEGG) | GO and unspecified pathway databases. | | 4. Background gene list | Not described. Used target genes from ≥4 algorithms, no broader list. | | 5. Statistical test (e.g., hypergeometric, Fisher’s exact) | Not described. | | 6. False discovery rate (FDR) correction used | Not described. |