MONGKIE¶
MONGKIE is a software platform for interactive visualization and analysis of complex omics data in the context of biological networks.
- All components for visualization (e.g. Data-to-Visual mapping and Gene expression overlay), network analysis of defining subgroups, and functional interpretation of network modules can be easily threaded into a pipeline that allows user interaction at each step.
- It was built on top of the Plug-in architecture to support application extension by third-party developers.
Important
In the Case Study, we demonstrate how MONGKIE can be used to identify driver gene candidates and core regulatory modules in the study of TCGA Glioblastoma Multiforme (Brennan et al., 2013).
- 1. Installation
- 2. Tutorial
- 2.1. Import a GBM-altered network
- 2.2. Data-to-Visual mapping
- 2.3. Network clustering
- 2.4. Make a new network from a cluster
- 2.5. Import expression log2FCs in normal vs. tumor
- 2.6. Functional annotation of a cluster
- 2.7. Import expression profiles for 4 GBM subtypes
- 2.8. Save as a image, CSV files, GraphML, and a VLG (Visualized Graph) file
- 3. Case Study
- 4. Network Visualization
- 5. Network Analysis
- 6. Interaction Sources
- 7. User Interface
- 8. Import and Export
- 9. Implementation
- 10. References