Okay, let me try to figure out the answers to these questions about the pathway enrichment analysis in the article. First, I need to look through the Methods section and other sections for details on how the enrichment analysis was conducted. Question 1: What tool was used for pathway enrichment analysis? Looking through the Methods section, I remember the authors mentioned using STRING for protein-protein interaction networks. But that's about interactions, not enrichment. In the Results section, they talk about functional associations and biological pathways. Wait, in the Methods, under "Pathway and functional enrichment analysis," they might have specified a tool. Let me check again. Oh, in the Methods, under the subsection "Pathway and functional enrichment analysis," they wrote: "Functional enrichment analysis was performed using DAVID (Database for Annotation, Visualization and Integrated Discovery) v6.8." So the tool is DAVID. Question 2: Was a tool version number provided? Yes, they specified DAVID v6.8. So the answer is yes. Question 3: What gene set library was queried? DAVID uses multiple databases, including GO (Gene Ontology), KEGG, and others. The article mentions that they used DAVID, so the gene set libraries would be those integrated into DAVID. However, the specific libraries aren't listed here. The question asks for the library queried, like GO, KEGG, etc. Since DAVID is the tool, and it's a database that includes those, but the exact ones used aren't specified. The article might not mention specific libraries beyond stating DAVID. So the answer is DAVID's integrated databases (GO, KEGG, etc.), but since the question asks for the specific library (like GO), if they didn't specify which ones, then maybe it's not described. Wait, in the article, under the Results section when they talk about tyrosine ADP-ribosylation, they mention pathways but don't specify the exact libraries. However, in the Methods, it just says DAVID v6.8. So the answer might be that the gene set library isn't specified beyond DAVID. So the answer would be "not described" if they didn't list the exact ones. But DAVID uses GO, KEGG, etc., so maybe the answer is GO, KEGG, and others, but the article doesn't specify. The question asks what library was queried. If the authors didn't specify which libraries within DAVID were used, then the answer is not described. Alternatively, if DAVID is the tool, and the libraries are part of DAVID's database, then maybe it's acceptable to list them. However, the question is about the gene set library queried. Since the article doesn't explicitly list the libraries, the answer might be not described. Wait, the user's question is phrased as "what gene set library was queried (e.g., GO, KEGG, Reactome or other)?" So if the authors didn't specify, then the answer is not described. In the Methods, the authors only mention DAVID as the tool, not the specific gene sets. Therefore, the answer is not described. Question 4: Was a background gene list defined for pathway enrichment analysis? The Methods section under pathway analysis mentions that they used DAVID. Typically, DAVID uses a background gene list based on the species and the input genes. However, the article doesn't explicitly state whether they defined a specific background gene list. If they didn't mention it, then the answer is not described. The text says "Functional enrichment analysis was performed using DAVID (Database for Annotation, Visualization and Integrated Discovery) v6.8." There's no mention of a custom background. So the answer is not described. Question 5: What statistical test was used for enrichment analysis? DAVID commonly uses hypergeometric tests or Fisher's exact test for enrichment. The article doesn't specify the exact statistical test used. The Methods section doesn't mention the test, so the answer is not described. Question 6: Was false discovery rate correction used? The article doesn't mention any correction for multiple testing like FDR. The Methods section doesn't state whether they used FDR correction. Therefore, the answer is not described. So compiling all this, the answers would be: 1. DAVID 2. Yes (v6.8) 3. Not described 4. Not described 5. Not described 6. Not described 1. **What tool was used for pathway enrichment analysis?** **DAVID (Database for Annotation, Visualization and Integrated Discovery)** 2. **Was a tool version number provided?** **Yes (v6.8)** 3. **What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** **Not described** (The article mentions DAVID but does not specify the exact gene set libraries, such as GO, KEGG, or Reactome, used within DAVID for the analysis.) 4. **Was a background gene list defined for pathway enrichment analysis?** **Not described** (The article does not explicitly state whether a custom or specific background gene list was defined for the analysis.) 5. **What statistical test was used for enrichment analysis?** **Not described** (The article does not specify the statistical test, such as hypergeometric or Fisher’s exact test, used for enrichment analysis.) 6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** **Not described** (The article does not mention whether FDR correction or other methods were applied to control for multiple testing.) --- **Summary Table** | Question | Answer | |----------|--------| | 1. Tool used | **DAVID** | | 2. Version provided | **Yes (v6.8)** | | 3. Gene set library | **Not described** | | 4. Background gene list | **Not described** | | 5. Statistical test | **Not described** | | 6. FDR correction | **Not described** |