CluePedia is a plugin for Cytoscape that integrates experimental and in silico information to provide insights into biological pathways. It extends the functionality of ClueGO by allowing users to enrich networks with known and experimental data at the gene and miRNA levels. CluePedia offers several features, including: 1. **Gene/MiRNA Expression Visualization and Saving**: Users can visualize and save gene expression data, normalize and filter data, and extract specific expression levels. 2. **Gene/Interaction Enrichment**: CluePedia provides statistical tests (Pearson correlation, Spearman’s rank, Distance correlation, and Maximal Information Coefficient) to calculate correlation weights from custom data. It allows users to add, remove, and update nodes and edges in the network. 3. **Known and Custom Interactions**: The plugin includes precompiled interaction files from sources like STRING, miRBase, and miRRecords. Users can also create custom interaction files using experimental data. 4. **Network Manipulation**: Features like "Enrich," "Add," "Remove," and "Network Update" allow users to manipulate the network structure. 5. **Data Format and Publicly Available Data**: CluePedia supports various data formats and can import publicly available expression data from repositories like GEO and ArrayExpress. 6. **Organism and ID Types**: The plugin supports multiple organisms and automatically recognizes various gene and protein identifiers. 7. **Ontologies and Data Sources**: CluePedia and ClueGO use ontologies from sources like GO, KEGG, REACTOME, and STRING, which are regularly updated. CluePedia and ClueGO can be used together to create nested networks and extract genes from pathways, providing a comprehensive tool for biological network analysis.CluePedia is a plugin for Cytoscape that integrates experimental and in silico information to provide insights into biological pathways. It extends the functionality of ClueGO by allowing users to enrich networks with known and experimental data at the gene and miRNA levels. CluePedia offers several features, including: 1. **Gene/MiRNA Expression Visualization and Saving**: Users can visualize and save gene expression data, normalize and filter data, and extract specific expression levels. 2. **Gene/Interaction Enrichment**: CluePedia provides statistical tests (Pearson correlation, Spearman’s rank, Distance correlation, and Maximal Information Coefficient) to calculate correlation weights from custom data. It allows users to add, remove, and update nodes and edges in the network. 3. **Known and Custom Interactions**: The plugin includes precompiled interaction files from sources like STRING, miRBase, and miRRecords. Users can also create custom interaction files using experimental data. 4. **Network Manipulation**: Features like "Enrich," "Add," "Remove," and "Network Update" allow users to manipulate the network structure. 5. **Data Format and Publicly Available Data**: CluePedia supports various data formats and can import publicly available expression data from repositories like GEO and ArrayExpress. 6. **Organism and ID Types**: The plugin supports multiple organisms and automatically recognizes various gene and protein identifiers. 7. **Ontologies and Data Sources**: CluePedia and ClueGO use ontologies from sources like GO, KEGG, REACTOME, and STRING, which are regularly updated. CluePedia and ClueGO can be used together to create nested networks and extract genes from pathways, providing a comprehensive tool for biological network analysis.