Okay, let me tackle this step by step. The user wants me to figure out how the pathway enrichment analysis was conducted in the provided scientific article. They have six specific questions about the methods used. Since the user mentioned that the Methods section might have the info, but also other sections, I need to look through the entire article for clues. First, I'll start by reading through the provided article text carefully. The article is about a proteomics study on myofascial trigger points and the effects of dry needling. The results section mentions pathway enrichment analysis, specifically referring to KEGG pathways. For example, in the Results section, they talk about "enriched signaling pathways" like glycolysis/gluconeogenesis, glucagon signaling, etc., which are KEGG pathways. Looking at the Methods section (since the user specified to check there first), but in the provided text, the Methods might not be fully included. Wait, the user provided the entire article's text? Let me check again. The given text includes an Abstract, Introduction, Results, Discussion, Conclusion, and Acknowledgments. The Methods section isn't explicitly present here. Hmm, that complicates things. The user says "the Methods section, but information can also be found in other sections." So, perhaps the Methods weren't included in the provided text, but the Results or other sections mention the tools and methods used. In the Results section, when discussing the pathway analysis, they mention "pathway enrichment analysis" and specifically reference KEGG pathways. The term "enriched signaling pathways" is used, which is a common phrase in KEGG analysis. The specific pathways listed (like glycolysis/gluconeogenesis) are indeed part of KEGG. The question is about the tool used. Tools like DAVID, Enrichr, ClusterProfiler, or others are common for KEGG enrichment. The article doesn't explicitly name the tool. Let me search the text again. Scanning through the provided text, the only mention related to enrichment is in the results: "pathway enrichment analysis" without specifying the tool. The references cited (like Simons et al) might not be about the tool. The conclusion mentions "enriched signaling pathways" again but no tool name. Since the user's provided text doesn't mention the tool, I have to note that it's not described. Similarly, version numbers (question 2) would also not be mentioned if the tool isn't specified. For the gene set library (question 3), since they refer to KEGG pathways (glycolysis, glucagon signaling are KEGG terms), the library is KEGG. Regarding a background gene list (question 4), usually, in enrichment analysis, the background is the entire set of genes/proteins analyzed. The article might not specify this, so it's possibly not described here. Statistical test used (question 5): Common tests include hypergeometric test or Fisher's exact test for overrepresentation. Since they don't specify, perhaps not described. False discovery rate (FDR) correction (question 6): Often, FDR (like Benjamini-Hochberg) is applied. The article mentions "false positives" in the limitations but doesn't state whether FDR was used. Wait, in the results, they might have used terms like adjusted p-values or FDR, but in the provided text, I don't see such details. The user's text says "enriched signaling pathways" but doesn't specify statistical tests or corrections. So, summarizing: 1. Tool: Not described in the provided text. 2. Version: Not applicable if tool isn't mentioned. 3. Gene set library: KEGG (since they mention KEGG pathways explicitly). 4. Background gene list: Not described. 5. Statistical test: Not specified. 6. FDR correction: Not mentioned. I need to check again if any part mentions DAVID or another tool. The references given (like 30,31 etc.) might be in the bibliography, but since the references aren't provided here, I can't check. The article's conclusion says "pathway enrichment analysis" without more details. Therefore, answers are as above. 1. **What tool was used for pathway enrichment analysis?** Not described. The article mentions pathway enrichment analysis and references KEGG pathways but does not specify the tool (e.g., DAVID, ClusterProfiler, Enrichr) used. 2. **Was a tool version number provided?** Not described. Since the tool itself is not specified, the version number is also not mentioned. 3. **What gene set library was queried (e.g., GO, KEGG, Reactome, or other)?** The analysis used the **KEGG** pathway library, as the results explicitly mention KEGG pathways (e.g., glycolysis/gluconeogenesis, glucagon signaling). 4. **Was a background gene list defined for pathway enrichment analysis?** Not described. The article does not specify whether a background gene list was used or how it was defined. 5. **What statistical test was used for enrichment analysis?** Not described. Common tests like the hypergeometric test or Fisher’s exact test are typically used for overrepresentation analysis, but the article does not specify the statistical method. 6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** Not described. While false discovery rate (FDR) correction is standard practice, the article does not mention whether FDR (e.g., Benjamini-Hochberg) was applied. --- ### Summary Table: | Question | Answer | |----------|--------| | 1. Tool used? | Not described. | | 2. Tool version? | Not described. | | 3. Gene set library? | KEGG. | | 4. Background gene list defined? | Not described. | | 5. Statistical test used? | Not described. | | 6. FDR correction used? | Not described. |