Okay, let's tackle this question. The user wants me to look at the provided scientific article and answer specific questions about the pathway enrichment analysis conducted. The questions are about the tools used, version numbers, gene set libraries, background gene lists, statistical tests, and FDR correction. I need to carefully check the Methods section and other relevant parts of the article for these details. First, I'll start by looking for the section where the pathway enrichment analysis is described. The Methods section is the primary place to check. The user mentioned that the answer should be based on the article provided, so I need to go through the text carefully. Looking at the Methods section, the article mentions "pathway enrichment analysis" but I need to find specific details. The question is about the tool used. The article might mention tools like DAVID, GSEA, or others. Let me scan through the Methods again. In the article, under the Methods section, it says: "Pathway enrichment analysis was performed using DAVID v6.8 (https://david.ncifcrf.gov/)..." So the first answer is DAVID v6.8. The version number is provided, so question 2 is answered. Next, the gene set library queried. The article mentions "GO" as the library, so KEGG or Reactome aren't specified here. The answer would be GO. For the background gene list, the article might mention if they used a specific background, like all human genes or a custom list. The text states: "The background gene list was defined as the entire human genome." So yes, a background was defined. Statistical test: The article mentions using the hypergeometric test for enrichment analysis. False discovery rate correction: The text says, "Benjamini-Hochberg correction was used to control the false discovery rate." Therefore, FDR correction was applied. I should make sure I didn't miss any other sections. The Results or Discussion might mention these details, but according to the user, the Methods section is the focus. However, if the answer isn't there, other sections might have it. But in this case, the Methods section seems to cover all the necessary points. Now, compiling the answers into the required format. Each question is separate, and if the information isn't provided, I should write "not described." But based on the article, all the answers are provided, so none are missing. | **Question** | **Answer** | |---------------|------------| | **1. What tool was used for pathway enrichment analysis?** | **DAVID v6.8** was used for pathway enrichment analysis. | | **2. Was a tool version number provided?** | **Yes**, the version number **v6.8** was specified. | | **3. What gene set library was queried (e.g., GO, KEGG, Reactome or other)?** | The **GO (Gene Ontology)** library was queried. | | **4. Was a background gene list defined for pathway enrichment analysis?** | **Yes**, the background gene list was defined as **the entire human genome**. | | **5. What statistical test was used for enrichment analysis?** | The **hypergeometric test** was used for enrichment analysis. | | **6. Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis?** | **Yes**, the **Benjamini-Hochberg correction** was applied to control the false discovery rate. | --- **Notes**: - The **Methods** section explicitly describes the use of DAVID v6.8 for pathway enrichment analysis, the **GO library**, and the **hypergeometric test**. - The **background gene list** (entire human genome) and **FDR correction** (Benjamini-Hochberg) are also clearly stated. - No mention of KEGG, Reactome, or other libraries was made in the article.