Okay, let's tackle this question about the pathway enrichment analysis in the given article. The user wants me to answer six specific questions based on the Methods section and other relevant parts. First, I need to figure out what tools were used for the pathway enrichment analysis. The Methods section under "Functional enrichment analysis" mentions DAVID version 6.8 and WebGestalt 2017. So for question 1, the answer is both DAVID and WebGestalt. Question 2 asks if a tool version number was provided. The article does specify version numbers for both tools: DAVID 6.8 and WebGestalt 2017. So that's a yes. Next, question 3 is about the gene set library queried. The DAVID analysis includes GO terms (BP, CC, MF) and KEGG pathways. WebGestalt is also used for KEGG pathways. So the libraries are GO and KEGG. For question 4, the background gene list. The article states that the Bos taurus genome was used as background for both analyses. So the answer is yes, and it's the Bos taurus genome. Question 5 is about the statistical test. The article mentions an Overrepresentation Enrichment Analysis (ORA) was performed by DAVID and WebGestalt. ORA typically uses hypergeometric tests or similar, but the article doesn't specify the exact test. So the answer here is not described, since the specific test isn't mentioned. Lastly, question 6: was FDR correction used? The article says DAVID used FDR of 5%, and WebGestalt also used FDR of 5%. So yes, FDR correction was applied to control false positives. I need to make sure I didn't miss any details. Let me double-check the Methods section. The DAVID part mentions FDR 5%, and WebGestalt also mentions FDR 5%. The tools and versions are clearly stated. The gene set libraries are GO and KEGG. Background is Bos taurus. The statistical test isn't specified beyond ORA. All six questions seem covered. | **Question** | **Answer** | |--------------|------------| | 1. What tool was used for pathway enrichment analysis? | DAVID (version 6.8) and WebGestalt 2017. | | 2. Was a tool version number provided? | Yes. DAVID version 6.8 and WebGestalt 2017 were explicitly mentioned. | | 3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)? | Gene Ontology (GO) categories (biological process [BP], cellular component [CC], molecular function [MF]) and KEGG pathways. | | 4. Was a background gene list defined for pathway enrichment analysis? | Yes. The *Bos taurus* genome was used as the background gene list for both DAVID and WebGestalt analyses. | | 5. What statistical test was used for enrichment analysis? | Overrepresentation Enrichment Analysis (ORA) was performed, but the specific statistical test (e.g., hypergeometric test) is **not described** in detail. | | 6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis? | Yes. Both DAVID and WebGestalt applied false discovery rate (FDR) correction with a threshold of 5%. |