Alright, so I need to figure out the answers to these six questions about the pathway enrichment analysis from the provided scientific article. Let me go through each question one by one and see what information I can extract. 1. **What tool was used for pathway enrichment analysis?** - The Methods section of the article isn't explicitly detailed here, but in the Abstract and other sections, they mention using "String" for protein interaction network analysis. However, String is primarily a database for protein interactions rather than a pathway enrichment tool like GSEA or DAVID. Looking through the text, I don't see any mention of specific tools like Metascape, Enrichr, or others used for pathway analysis. So it seems they might not have explicitly stated the tool used for pathway enrichment. 2. **Was a tool version number provided?** - There's no indication in the provided text that a version number was mentioned. The focus is more on the biological findings rather than the specifics of the tools and their versions. 3. **What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** - The article discusses functional categories like "alternative splicing," "phosphoproteins," "acetylation," etc., which are typically part of Gene Ontology (GO) terms. They also mention specific pathways such as the Wnt signaling pathway and processes related to ubiquitination, but there's no explicit mention of using KEGG or Reactome databases. So it seems they might have used GO for their analysis. 4. **Was a background gene list defined for pathway enrichment analysis?** - The article doesn't describe whether a specific background gene list was used. They mention selecting 10 paired bands with obvious differences for MS, which suggests they had a focused dataset but don't specify if this was used as the background or how it was applied in the analysis. 5. **What statistical test was used for enrichment analysis?** - The text doesn’t provide details on the statistical methods used for pathway enrichment. They discuss functional categories and biological processes but without mentioning specific tests like hypergeometric test, Fisher's exact test, etc. 6. **Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** - There’s no information provided about whether any multiple testing corrections, such as FDR or Bonferroni, were applied. The article focuses more on the results and biological implications rather than the statistical methods used. Putting it all together, it seems the article doesn't provide detailed methodology for their pathway enrichment analysis beyond using String for interaction networks and discussing GO-like categories. Here is a structured summary of the findings based on the provided questions: 1. **Tool Used**: The tool used for pathway enrichment analysis isn't explicitly mentioned in the article. String was referenced but primarily for protein interactions, not pathway enrichment. 2. **Version Number Provided**: No version number for any tool was provided in the text. 3. **Gene Set Library Queried**: The analysis appears to have used Gene Ontology (GO) terms based on the functional categories discussed, such as "alternative splicing" and "phosphoproteins." 4. **Background Gene List Defined**: There is no mention of a background gene list being defined for the pathway enrichment analysis. 5. **Statistical Test Used**: The specific statistical test used for enrichment wasn't detailed in the article. 6. **False Discovery Rate Correction**: No information was provided about whether false discovery rate correction or other multiple testing adjustments were applied. This summary highlights that while some elements of the methodology can be inferred, many details about the pathway enrichment analysis remain unspecified in the article.