Alright, I'm trying to figure out how to answer these questions about the pathway enrichment analysis from the given scientific article. Let me read through the relevant sections carefully. First, looking at the Methods section under "GO enrichment analysis" and "KEGG pathways," it mentions that GOseq R package was used for GO enrichment with a corrected P-value cutoff of 0.5. Then, KOBAS software was used to test statistical enrichment in KEGG pathways. So, I can note that KOBAS is the tool for KEGG. Next, checking if any version numbers were provided. The article doesn't mention specific versions for GOseq or KOBAS, so I think it's safe to say version numbers aren't described. For the gene set libraries, since they used GO and KEGG, those are the ones queried. No mention of Reactome or others, so that's straightforward. Regarding a background gene list, the article doesn’t specify if one was defined, especially for KOBAS. It only talks about DEGs being tested against these pathways without details on the background, so I'll note it as not described. Statistical tests: GOseq uses a method based on the Wallenius non-central hypergeometric distribution, but the article doesn't explicitly state this. For KOBAS, it's likely using some form of statistical testing, perhaps hypergeometric, but it's also not detailed. Since the article doesn’t specify, I'll say it's not described. Lastly, false discovery rate correction: The DESeq analysis uses Benjamini-Hochberg’s approach for FDR correction with an adjusted P-value ≤0.01. However, it's unclear if this same correction was applied during pathway enrichment in GOseq and KOBAS. The article mentions a corrected P-value for GO but doesn’t specify if FDR was used, so I can't confirm FDR correction for pathways. Putting it all together, the tools are GOseq and KOBAS without version numbers, using GO and KEGG libraries. No background list is defined, statistical tests aren't described, and while FDR is used in DESeq, its application to pathway analysis isn't clear. | Question | Answer | |----------|--------| | **1. What tool was used for pathway enrichment analysis?** | GOseq R package and KOBAS software were used. | | **2. Was a tool version number provided?** | No, the article does not provide specific version numbers for these tools. | | **3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** | The libraries queried were Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). | | **4. Was a background gene list defined for pathway enrichment analysis?** | Not described. The article does not specify whether a background gene list was defined. | | **5. What statistical test was used for enrichment analysis?** | Not described. The specific statistical tests used by GOseq and KOBAS are not detailed in the article. | | **6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** | False discovery rate (FDR) correction is mentioned for DESeq analysis, but it is unclear if FDR correction was specifically applied during pathway enrichment analysis with GOseq and KOBAS. The article does not provide explicit details on this aspect. |