- The [http://bioinformatics.oxfordjournals.org/content/29/21/2757.short TieDIE algorithm] computes a subnetwork of gene and protein interactions that connect genomic perturbations to gene expression changes characteristic of cancer subtypes. The pathways derived in this way predict interlinking genes that may correspond to essential components of cancer signaling and may provide a mechanistic explanation of tumor behavior and suggest subtype-specific drug targets.
- If you are interested in the evolution of subnetwork, you should generate various subnetworks with sizes varying from 0 to a desired size. The captured snapshots are given
input to CyAnimator Cytoscape app for obtaining the animation. Here is a sample [https://youtu.be/6nXR4tOWH7k video] on the same. This animation has won first prize in Cytoscape animation challenge.
## Installation & Usage
- Import network file using File -> Import ->Network -> File
- Import table file using File -> Import -> Table -> File (Import table data as node table columns)
- Sample network file, upstream table file, downstream table file can be downloaded from
[https://drive.google.com/folderview?id=0B7tcNKEe4Fl3akdTV19ZUkVLQmc&usp=sharing here ]
- Click Apps -> TieDIE to get the user interface loaded in the control panel of Cytoscape.
- Select the appropriate columns using comboboxes
- Select the way of diffusion using radio buttons (Heat diffusion or pagerank)
- Select the size of subnetwork, default = 1.0
- Click the RUN button
- A new subnetwork is created programmatically and corresponding visualization changes in the original network
### Visualization Guide
- Source nodes in input network : Red bordered nodes (octagon shape)
- Target nodes in input network : Red colored nodes (octagon shape)
- Linker nodes in input network : Orange bordered nodes (octagon shape)
- Linker edges in input network : Thick Orange edges
- Source nodes in extracted subnetwork : Red bordered nodes
- Target nodes in extracted subnetwork : Red colored nodes
- Linker nodes in extracted subnetwork : Orange colored nodes
- Linker edges in extracted subnetwork : Thick Orange edges
TieDIE app for Cytoscape has been developed by Srikanth under the mentorship of Evan, Thanks to GSOC2014 and NRNB.