Table 1.
Comparison with other web-based network analysis tools
| Tools | NetworkAnalyst | InnateDB | STRING | R Spider | VisANT |
|---|---|---|---|---|---|
| Implementation | Web | Web | Web | Web | Java Applet |
| Supported organisms | Human and mouse | Human, mouse and cow | >1100 organisms | Six model organisms | 112 species |
| Data processing | |||||
| Input | Gene or protein list, single or multiple expression data | Gene or protein list | Protein list | Gene or protein list | Gene or protein list |
| Probe annotation | Affymetrix, Illumina, Agilent | No | No | Affymetrix | No |
| Differential analysis | Yes | No | No | No | No |
| Network construction | |||||
| Interaction type | PPI | PPI | PPI | Metabolic, signaling | PPI, metabolic, drug, disease |
| Interaction distance | Zero, first or higher order | Zero or first order | Zero, first or higher order | Zero, first or second order | Zero, first or higher order |
| Network analysis and visualization | |||||
| Interactive visualization | Yes | Delegated to Cytoscape | Built-in visualization tools are suitable for small networks; Cytoscape plugins are available for visualizing large networks | Yes | |
| Topology analysis | Yes | Yes | |||
| Module analysis | Yes | Yes | |||
| Functional analysis | Yes | Yes | |||
| Result download | Edge list, PNG, PDF, GraphML | Edge list, VisML, SVG | |||
The URL for each tool is given below:
NetworkAnalyst: http://www.networkanalyst.ca.
InnateDB: http://www.innatedb.com.
STRING: http://string-db.org.
VisANT: http://visant.bu.edu/.