Table 1.
A selection of network-based multi-omics knowledge bases, visualization tools and online resources.
| Network visualization | Analysis tools | Project omics data onto network | Biological entities | Implementation | Reference | |
|---|---|---|---|---|---|---|
| BioCyc | x | Enrichment analysis Flux analysis | x | genes proteins metabolites | online | [206] |
| KEGG | x | - | x | genes enzymes metabolites | online KEGGscape+ CytoKegg+ | [76] |
| Reactome | x | Enrichment analysis ID mapping | x | proteins metabolites diseases | online ReactomeFIViz+ | [78] |
| Recon3D | x | x | genes metabolites | online | [82] | |
| PathwayCommons | x | Enrichment analysis | - | proteins metabolites drugs | online R CyPath2+ | [207] |
| WikiPathways | x | - | - | genes proteins metabolites | online WikiPathways+ | [208,209] |
| NDEx | x | Neighborhood search | - | various** | online CyNDEx-2+ | [190,210,211] |
| PaintOmics3 | x | Clustering Correlation analysis Enrichment analysis ID mapping | x | genes proteins metabolites | online | [68] |
| MetaboAnalyst | x | Enrichment analysis ID mapping Shortest path analysis | x | genes metabolites | online R | [84] |
| OmicsNet | x | Clustering Enrichment analysis Shortest path analysis | x | genes proteins TFs miRNAs metabolites | online | [169] |
| MetExplore | x | Enrichment analysis Flux analysis ID mapping Shortest path analysis | x | genes enzymes metabolites | online | [212] |
| ConsensusPathDB | x | Clustering Enrichment analysis Shortest path analysis | x | genes proteins metabolites | online | [167] |
| PathMe Viewer | x | Shortest path analysis | genes proteins metabolites | online | [213] | |
| MetScape | x | Correlation analysis Enrichment analysis | x | genes enzymes metabolites | MetScape+ | [214,215] |
**
no restrictions
+
Cytoscape Application [216]