Okay, so I'm trying to figure out how pathway enrichment analysis was conducted in this scientific article. The user has provided a detailed abstract and sections like Author Contributions, Conflict of Interest Statement, Acknowledgments, but not the Methods section where such details are usually found. First, I need to check if there's any mention of tools or methods related to pathway enrichment anywhere in the provided text. Looking through the Abstract, Results, Discussion, Conclusion, etc., I can see that the authors mention using microarray analysis and some specific genes like FOS being up-regulated. They also talk about the AMPH addiction pathway being involved. In the Abstract under "Results," they note that FOS expression was validated in another dataset. The Discussion section mentions that FOS is connected to pathways like AP-1, which regulates MMP1. However, there's no explicit mention of how they performed the pathway enrichment analysis—what tool they used, whether they used KEGG, GO, or another database. The Methods section isn't provided here, so I don't have access to that part where these details are usually explained. Without that information, it's impossible to know which tool was used for the analysis, whether a specific version was mentioned, what gene set libraries were queried, if a background list was defined, the statistical tests applied, or if they controlled for false discoveries using FDR. So, based on the available text, all these points remain unclear. The authors didn't provide any details about their pathway enrichment methodology in the sections that are accessible here. | Question | Answer | |-----------------------------------------------|----------------------------| | What tool was used for pathway enrichment analysis? | Not described | | Was a tool version number provided? | Not described | | What gene set library was queried (e.g., GO, KEGG, Reactome or other)? | Not described | | Was a background gene list defined for pathway enrichment analysis? | Not described | | What statistical test was used for enrichment analysis? | Not described | | Was false discovery rate correction used to control the number of false positives in the pathway enrichment analysis? | Not described | The article does not provide specific details about the methodology used for pathway enrichment analysis.