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).

Table of Contents

• 1. Installation
  • 1.1. System Requirements
  • 1.2. ZIP Distributions
  • 1.3. Installable Packages
  • 1.4. User Directories
• 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
  • 3.1. Cancer omics data
  • 3.2. Extraction of a GBM-altered network
  • 3.3. Statistical test for significant linkers
  • 3.4. Network clustering
  • 3.5. Results
• 4. Network Visualization
  • 4.1. Visual representation of biological entities and interactions
  • 4.2. Pathway visualization
  • 4.3. Visual editor UI and Data-to-Visual mapping
  • 4.4. Exploring network
  • 4.5. Graph layouts
• 5. Network Analysis
  • 5.1. Network clustering
  • 5.2. Gene expression overlay
  • 5.3. Over-representation analysis
• 6. Interaction Sources
  • 6.1. hiPathDB
  • 6.2. Interaction Manager
• 7. User Interface
• 8. Import and Export
• 9. Implementation
  • 9.1. Plug-in architecture
  • 9.2. RESTFul Web service API
• 10. References