Okay, so I need to figure out how the authors conducted their pathway enrichment analysis in this study. Let me start by reading through the article carefully. The article discusses using RNA-Seq on whole blood from ARDS patients after HSCT and comparing it to non-HSCT ARDS patients. They found differentially expressed genes related to immune responses and interferon signaling. Looking for details about pathway enrichment analysis, I'll check the Methods section first. Unfortunately, the provided text doesn't include a detailed Methods section. It mainly describes the study's background, results, discussion, etc. In the Results section, they mention using DAVID Functional Annotation Clustering. So that answers question 1: the tool used was DAVID. The article doesn't specify the version of DAVID used, so I'll note that as not described for question 2. For gene set libraries, since they used DAVID, it typically uses GO (Gene Ontology) among others. The discussion mentions innate immune responses and type I interferon signaling, which are common in GO annotations. So I can infer they queried the GO library, so question 3 is GO. Regarding a background gene list, the article doesn't specify if they used one. RNA-Seq often uses all expressed genes as the background, but since it's not mentioned, I'll say not described for question 4. Statistical test: DAVID usually uses a modified Fisher's exact test or similar, but without specifics here, it's unclear. The article doesn't detail this, so question 5 is not described. For multiple testing correction, the Results mention FDR correction for gene expression analysis (FDR <0.05). It's likely they applied similar corrections to pathway enrichment, so I'll say yes to question 6. I think that's all I can gather from the provided text. | Question | Answer | |----------|--------| | **1. What tool was used for pathway enrichment analysis?** | DAVID Functional Annotation Clustering | | **2. Was a tool version number provided?** | Not described | | **3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** | 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 | | **6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** | Yes (FDR < 0.05) | This table collates the information gathered from the article regarding the pathway enrichment analysis methodology.