Okay, so I need to figure out how the authors conducted their pathway enrichment analysis based on this article. Let me start by looking through the Methods section since that's where such details are usually found. The Methods section here talks about sample preparation, mass spectrometry, data acquisition, and protein identification. They mention using MaxQuant for data analysis, but I don't see any specific tool named for pathway enrichment. They do reference additional files which include detailed methods, figures, tables, and pathway mappings, so maybe some info is there. Looking through the Results section, they discuss various biological processes affected in UC, such as metabolic pathways, ER stress, etc., but again, no mention of the tools used for enrichment analysis. The Discussion mentions possible applications and interpretations but doesn't go into methodological details about how they did the pathway analysis. The Additional Files section refers to two files: one with detailed methods, figures, tables, and pathway mappings (Additional file 1) and another with a complete list of proteins and GO term enrichments (Additional file 2). Since I don't have access to these files, I can only infer based on what's written in the main article. Given that, it seems the authors didn't specify which tool they used for pathway enrichment. They might have used something like DAVID or Metascape, but since it's not mentioned, I can't be sure. The same goes for the gene set library—they could have used GO, KEGG, Reactome, or a custom database, but without specifics, I don't know. Regarding the background gene list, usually, pathway analysis requires a reference or background set of genes. If they didn’t mention it, perhaps they used all identified proteins as the background. The statistical test isn't specified either—common ones include hypergeometric tests or Fisher's exact tests. They might have used one of these but didn't state which. On false discovery rate (FDR) correction, again, no details are given. It's a common practice to correct for multiple comparisons using FDR, especially in 'omics studies, but without explicit mention, I can’t confirm if they did it. So, putting this together, the article lacks specific details about the pathway enrichment analysis methods beyond what's implied by the results and additional files. Therefore, many of my answers will note that these details aren't described. | Question | Answer | |---------|--------| | 1. What tool was used for pathway enrichment analysis? | Not described. | | 2. Was a tool version number provided? | Not described. | | 3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)? | Not described. | | 4. Was a background gene list defined for pathway enrichment analysis? | Not described; possibly all identified proteins were used as the background. | | 5. What statistical test was used for enrichment analysis? | Not described; common tests like hypergeometric or Fisher's exact might have been used. | | 6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis? | Not described, though it's a common practice in such studies. | The article does not provide specific details about the tools, methods, or parameters used for pathway enrichment analysis beyond general implications from the results and supplementary materials.