Network Analysis, Visualization, & Graphing TORonto (NAViGaTOR)

Category Cross-Omics>Pathway Analysis/Gene Regulatory Networks/Tools

Abstract NAViGaTOR (Network Analysis, Visualization, & Graphing TORonto) is a software package for visualizing and analyzing protein-protein interaction networks.

NAViGaTOR can query OPHID / I2D - (online databases of interaction data) - and display networks in 2D or 3D.

To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D visualization system on multiple hardware platforms.

NAViGaTOR also provides analytical capabilities and supports standard import and export formats such as Gene Ontology (GO) and the Proteomics Standards Initiative (PSI).

NAViGaTOR Features/capabilities include:

1) NAViGaTOR combines a visualization system implemented in OpenGL with a graphical user interface (GUI) and analytical algorithms implemented in Java.

2) Networks can be loaded from a file (tab-delimited, NAViGaTOR XML, BioPAX or PSI formats), or can be generated dynamically by executing a ‘visual query’ to OPHID / I2D [Interologous Interaction Database -- an online database of known high-throughput and predicted protein-protein interactions (PPI’s) for human, rat, mouse, fly, worm, and yeast - (see G6G Abstract Number 20687)]; or cPath - (see G6G Abstract Number 20098).

NAViGaTOR XML - NAViGaTOR 2.0 has its own internal XML file format which represents networks in the XML format, and allows for the saving of all the network information, data and visualization features. 2.0 XML Files can be loaded and saved without any data loss.

NAViGaTOR 2.0 Text - NAViGaTOR supports fast tab-delimited import and export through the use of the ‘NAViGaTOR 2.0 Text’ format.

The files saved in this format can be loaded and edited into many software applications, such as TextPad and Microsoft Excel.

BioPAX and PSI-MI XML Files - BioPAX and PSI-MI XML files are two (2) formats for network representation that are supported in NAViGaTOR.

3) The NAViGaTOR workspace supports multiple network panels which can be manipulated by cutting, copying and pasting nodes and edges.

4) Networks can be exported in tab-delimited, NAViGaTOR XML, PSI, or Pajek formats, and multiple graphical formats (BMP, JPG, TIFF, SVG, and PDF).

Pajek - Pajek (Slovene word for Spider) is a program for Windows, for the analysis and visualization of large networks having some thousands or even millions of vertices.

5) Networks can be viewed in 2D and 3D.

6) Nodes can be positioned using a mixture of automatic force-directed layout and manual placement.

One of the automatic layout algorithms used is a multi-level force-directed layout algorithm called GRIP (Graph dRawing with Intelligent Placement) [Gajer and Kobourov, 8th Symposium on Graph Drawing (GD), 2000].

Because of the nearly linear time complexity of GRIP, NAViGaTOR can visualize full interactomes from I2D.

7) Subnetworks that are highly interconnected, and nodes that are hubs (i.e. that interact with many other nodes), can be automatically identified to aid analysis.

8) Groups of nodes can be collapsed into composite nodes, either manually, or in an automated fashion.

9) Subsets of a network can be bookmarked and manipulated using standard set operations, such as union, intersection and difference.

10) The opacity of nodes and edges can be adjusted to change the contrast of elements in the network and emphasize selected elements.

In protein-protein interaction networks, nodes represent proteins, and edges between nodes represent physical interactions between the proteins.

NAViGaTOR allows nodes and edges to be color-coded according to Gene Ontology (GO) - (a controlled vocabulary describing properties of genes) terms and according to experimentally-gathered information regarding the expression of, and correlations between, proteins.

Note: These visualizations (networks) can enable insights into the proteins that play key roles in diseases such as cancer.

System Requirements

NAViGaTOR can be installed and run on Microsoft Windows, Linux / UNIX, and Mac OS systems.

NAViGaTOR is written in Java and uses JOGL (Java bindings for OpenGL) to support scalability, highlighting or suppressing of information, and other advanced graphic approaches.

Manufacturer

Manufacturer Web Site NAViGaTOR

Price Contact manufacturer and NAViGaTOR is freely-downloadable for academic and Not-for-profit institutions.

G6G Abstract Number 20686

G6G Manufacturer Number 104263