Okay, let me go through this step by step. The user wants me to figure out how the pathway enrichment analysis was conducted in the provided scientific article. They have specific questions about the tools, versions, gene sets, background lists, statistical tests, and FDR correction. I need to look through the Methods section and other parts of the article to find the answers. First, looking at the Methods section. The user mentioned sections like 4.6 (Proteome Data Analysis) and 4.7 (Gene Coexpression Network Analysis), but maybe also others. Let me check each part. Starting with question 1: What tool was used for pathway enrichment analysis? In section 4.6, under Proteome Data Analysis, it says they mapped proteins to NCBI NR, Swiss-Prot/UniProt, GO, and KEGG databases. Then it mentions using Fisher’s exact test for calculating p-values and Q-values for FDR with the "q-value" R package. The enrichment analysis here is for GO terms and KEGGG pathways. The tool isn't explicitly named, but they mention using Fisher’s exact test. Wait, maybe the tool is part of the R package? Let me check again. The text says: "Using all the proteins as background, we used the numbers of differentially expressed proteins (DEPs) to calculate the p-value and Q-value..." So they might have used a custom script or an R package that does GO/KEGG enrichment with Fisher's exact test. The exact tool isn't named, like DAVID or clusterProfiler. Hmm, maybe they didn't specify the tool, just the statistical methods. Looking at question 2: Version number of the tool. Since the tool isn't named, probably not provided. Question 3: Gene set library. They mention GO and KEGG, so those are the libraries used. Question 4: Background gene list. The text says "using all the proteins as background", so the background was the entire set of proteins. Question 5: Statistical test. They mention Fisher’s exact test for p-values. Question 6: FDR correction. They mention Q-value calculated by the "q-value" R package, so yes, FDR correction was applied. Wait, the user also mentioned looking in other sections. Let me check the Results or elsewhere. The pathway enrichment is discussed in the Methods under proteome analysis. For the transcriptome (DEGs), maybe in another section? The DEGs are handled with NOIseq, but for enrichment, perhaps the same approach? Wait, in 4.6 they talk about proteome DEPs enrichment using Fisher's exact. But for genes, maybe they used a different method? Let me check the DEG analysis in 4.9? No, 4.9 is qRT-PCR. The DEGs are in 4.6? Wait, DEGs are in the transcriptome, but the pathway analysis for genes might be mentioned elsewhere. Wait, the question is about pathway enrichment in general. The article might have done both for proteomics and transcriptomics. Let me recheck 4.6 again. The proteome analysis section mentions GO and KEGG enrichment using Fisher's exact. For the transcriptome (genes), in the DEG section (4.6 is proteome; DEGs are in 4.9? No, looking at section 4.6 is proteome. The DEGs are probably analyzed with NOIseq, but their enrichment isn't detailed here? Wait, the question is about pathway enrichment, which might be in proteome analysis. Since the user's question is general about pathway enrichment, but the methods for DEGs and DEPs are separate. The proteome's enrichment is detailed in 4.6. The gene coexpression network (4.7) is different. The user's question is about pathway enrichment analysis. So, the main pathway analysis is in the proteome part. So for the proteomics, they used Fisher's exact test with GO and KEGG, with background as all proteins. The DEGs might not have had pathway analysis, or maybe it's implied? The user might be referring to both, but since the Methods for proteome is explicit, that's where the info is. So, compiling the answers: 1. Tool: Not explicitly named. They mention Fisher’s exact test and the "q-value" R package for Q-values, but the actual enrichment tool isn't specified. Maybe they used a custom script or an R package like clusterProfiler, but it's not stated. Wait, the text says "the numbers of differentially expressed proteins (DEPs) to calculate the p-value and Q-value, which represented the significance of the enriched GO terms/KEGG pathways and the false discovery rate (FDR), respectively. The p-values were calculated by Fisher’s exact test, and the Q-values were calculated by an R package named “q-value”." So the actual enrichment was done with Fisher's exact test, and the package for Q-value is separate. The tool for the enrichment analysis is not named. So the answer is that the tool isn't specified, but they used Fisher's exact test. Wait, but the question is about the tool (software) used. Since they didn't mention DAVID, clusterProfiler, or others, maybe the answer is "not described" but they used Fisher's exact test. Hmm, perhaps the tool is part of their own script, so the answer to question 1 would be "not described, but used Fisher’s exact test". But the user wants the tool name. Since it's not mentioned, I should say "not described". Wait, perhaps I missed something. Let me check again. In 4.6: "Using all the proteins as background, we used the numbers of differentially expressed proteins (DEPs) to calculate the p-value and Q-value..." So they might have used a custom approach. Alternatively, maybe they used an R package like GOstats or clusterProfiler. But since it's not stated, the answer is "not described". So answers: 1. Tool: Not described. 2. Version: Not applicable, since tool isn't named. 3. Gene set libraries: GO and KEGG. 4. Background: All proteins as background. 5. Statistical test: Fisher’s exact test. 6. FDR: Yes, using the "q-value" R package for Q-values (FDR <0.05). Wait, the question 6 is whether FDR correction was used. Since they mention Q-values (FDR) with threshold <0.05, yes. So to answer each question: 1. What tool was used for pathway enrichment analysis? The article does not explicitly name the tool. They mention using Fisher’s exact test and the "q-value" R package for FDR, but the specific enrichment tool (e.g., clusterProfiler, DAVID) isn't stated. So answer: Not described. 2. Tool version: Not provided, as the tool isn't named. 3. Gene set libraries: GO and KEGG. 4. Background gene list: All proteins were used as the background. 5. Statistical test: Fisher’s exact test. 6. FDR correction: Yes, using the "q-value" R package to calculate Q-values with FDR <0.05. I need to make sure I didn't miss any mentions. The GO and KEGG mappings are mentioned, but the actual enrichment tool isn't. So the answers are as above. 1. **Tool used for pathway enrichment analysis**: Not described. *Explanation*: The article mentions using Fisher’s exact test and the "q-value" R package for FDR correction but does not explicitly name the specific tool or software (e.g., DAVID, clusterProfiler) used for pathway enrichment analysis. 2. **Tool version number provided**: Not applicable. *Explanation*: Since the tool is not named, no version number is provided. 3. **Gene set library queried**: GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes). *Explanation*: Proteins were mapped to the GO and KEGG databases for enrichment analysis. 4. **Background gene list defined**: Yes, all proteins were used as the background. *Explanation*: The text states, "using all the proteins as background," meaning the entire proteome served as the reference set. 5. **Statistical test used**: Fisher’s exact test. *Explanation*: The article explicitly states that p-values were calculated using Fisher’s exact test for enrichment analysis. 6. **False discovery rate (FDR) correction**: Yes, using the "q-value" R package. *Explanation*: Q-values were calculated with the "q-value" R package to control FDR, with a significance threshold of FDR < 0.05.