Table 1. Comparison of OmicsNet with other network visualization tools.
| Tools | OmicsNet | 3DScapeCS | BioLayout3D | Arena3D | NAViGaTOR |
|---|---|---|---|---|---|
| Platform | Web | Cytoscape plug-in | Standalone | Standalone | Standalone |
| Inputs | One or more lists of genes, proteins, TFs, miRNAs, metabolites; Or graph files (.txt, .sif, graphml) | List of genes, multiple graph files; time-series data | List of genes, Multiple graph files, expression matrix | Multiple graph files; time-series data | List of genes, multiple graph files |
| Network Construction and Integration | |||||
| Built-in database support | Yes | - | Yes | - | Yes |
| Network integration | Up to three types of interactions | - | - | - | - |
| Network Visualization and Analysis | |||||
| 3D visualization | Yes | Yes | Yes | Yes | Yes |
| Perspective layout | Yes | - | - | Yes | - |
| Spherical layout | Yes | - | - | - | - |
| Node drag-drop | Yes | - | 2D only | - | Yes |
| Enrichment Analysis | GO, KEGG, Reactome, PANTHER | - | - | - | - |
| Module Detection | Yes | - | - | - | - |
The URL for each tool is given below the table (note, evaluation for 3DScapeCS is based on functions offered by the plug-in itself).
• OmicsNet: http://omicsnet.ca/.
• 3DScapeCS: http://scape3d.sourceforge.net/.
• BioLayout3D: https://kajeka.com/graphia-professional/.
• Arena3D: http://arena3d.org/.
• NAViGaTOR: http://ophid.utoronto.ca/navigator/.