Okay, so I need to figure out how to answer these six questions about the pathway enrichment analysis in this scientific article. Let me start by reading through the Methods section carefully because that's where such details are usually found. First question: What tool was used for pathway enrichment analysis? Looking at the Methods section, I see they mention using Fisher’s exact test and an R package called “q-value” for calculating Q-values. But wait, do they specify a particular tool like DAVID or Metascape? Hmm, in section 4.6, under proteome data analysis, they talk about mapping proteins to databases including GO and KEGG. Then, using Fisher’s exact test and an R package for FDR. So the tools are Fisher's exact test and the q-value R package. Second question: Was a tool version number provided? I don't see any version numbers mentioned for these tools in the Methods section or elsewhere. They just mention “Fisher’s exact test” and the R package named “q-value”, but no specific versions. Third question: What gene set libraries were queried? In section 4.6, they mention mapping proteins to GO and KEGG databases. So the gene sets are from Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Fourth question: Was a background gene list defined for pathway enrichment analysis? The article says, "using all the proteins as background". That suggests they used the entire set of identified proteins as the background list. Fifth question: What statistical test was used for enrichment analysis? They explicitly mention Fisher’s exact test in section 4.6, so that's clear. Sixth question: Was false discovery rate correction used to control false positives? Yes, they used Q-values calculated by the q-value R package, which is a method for FDR correction. So FDR was indeed applied with a threshold of <0.05. **Answer:** 1. **Tool Used:** Fisher’s exact test and the R package "q-value". 2. **Tool Version Number:** Not described. 3. **Gene Set Libraries:** Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). 4. **Background Gene List:** Yes, they used all identified proteins as the background. 5. **Statistical Test:** Fisher’s exact test. 6. **FDR Correction:** Yes, FDR was applied using Q-values with a threshold of <0.05. | Question | Answer | |--------------------------------------------|----------------------------------------------------------------------------------------| | 1. Tool Used for Pathway Enrichment Analysis | Fisher’s exact test and the R package "q-value" | | 2. Was a Tool Version Number Provided? | Not described | | 3. Gene Set Libraries Queried | Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) | | 4. Background Gene List Defined | Yes, all identified proteins were used as the background | | 5. Statistical Test Used for Enrichment | Fisher’s exact test | | 6. FDR Correction Applied | Yes, using Q-values with an FDR threshold of <0.05 |