CluePedia is a Cytoscape plugin that integrates experimental and in silico data to provide insights into biological pathways. It extends the functionality of ClueGO by allowing analysis down to genes and miRNAs. CluePedia calculates statistical dependencies (correlation) for markers of interest from experimental data, using four tests: Pearson correlation, Spearman's rank, Distance correlation, and Maximal Information Coefficient. It also allows visualization and analysis of gene/miRNA expression data, interaction networks, and pathway information. CluePedia provides features such as expression data visualization, gene/interaction enrichment, and interaction data visualization. It supports both experimental and in silico interaction data, and allows users to update and download interaction data for other organisms. CluePedia also integrates with the Cerebral layout for visualizing cellular localization. The plugin includes an ID index file for fast analysis and supports various data formats. CluePedia and ClueGO work together within Cytoscape, and both require specific system requirements, including Java and Cytoscape versions. The documentation provides detailed instructions on installation, usage, and features of CluePedia.CluePedia is a Cytoscape plugin that integrates experimental and in silico data to provide insights into biological pathways. It extends the functionality of ClueGO by allowing analysis down to genes and miRNAs. CluePedia calculates statistical dependencies (correlation) for markers of interest from experimental data, using four tests: Pearson correlation, Spearman's rank, Distance correlation, and Maximal Information Coefficient. It also allows visualization and analysis of gene/miRNA expression data, interaction networks, and pathway information. CluePedia provides features such as expression data visualization, gene/interaction enrichment, and interaction data visualization. It supports both experimental and in silico interaction data, and allows users to update and download interaction data for other organisms. CluePedia also integrates with the Cerebral layout for visualizing cellular localization. The plugin includes an ID index file for fast analysis and supports various data formats. CluePedia and ClueGO work together within Cytoscape, and both require specific system requirements, including Java and Cytoscape versions. The documentation provides detailed instructions on installation, usage, and features of CluePedia.