Table 3. Analysis and display tools in the main metabolic databases.
Terms used in the table include Enrichment analysis: a tool for computing statistical enrichment of data sets, e.g., is a given set of genes enriched for known genes categories or for pathways. Choke point analysis: a tool for computing locations of metabolic choke points, which may identify potential drug targets. Metabolite Tracing: visual tracing of metabolites through metabolic network. Path Search: a tool that finds paths in the network that connect two user-specified metabolites. Reachability analysis: a tool that determines if the network can produce specified products from specified input compounds.
| MetaCyc | KEGG | Model SEED | Reactome | BiGG | |
|---|---|---|---|---|---|
| Genome Browser | YES | YES | |||
| Regulatory Network Browser | YES | ||||
| Full Metabolic Map Browser | YES | YES | YES | YES1 | YES |
| Zoomable Metabolic Map | YES | YES | YES | ||
| Paint Data onto Metabolic Map | YES | YES | YES1 | ||
| Pathway Diagrams | YES | YES | YES | YES | |
| Paint Data onto Pathway Diagram | YES | YES | YES | ||
| Automatic Pathway Layout | YES | ||||
| Pathway Diagrams Include Metabolite Structures |
YES | YES | |||
| Gene/Protein Page | YES | YES | YES | YES | |
| Metabolite Page | YES | YES | YES | YES | |
| Reaction Page | YES | YES | YES | YES | |
| Operon Page | YES | ||||
| Enrichment Analysis | YES | YES | |||
| Flux Balance Analysis | YES | YES | YES | ||
| Choke Point Analysis | YES | ||||
| Dead-End Metabolite Analysis | YES | ||||
| Metabolite Tracing Tool | YES | ||||
| Path Search Tool | YES | YES | YES | ||
| Reachability Analysis Tool | YES | YES | |||
| Pathway MultiSearch | YES | YES | |||
| Compound MultiSearch | YES | YES | YES | ||
| Substructure Search | YES | YES | |||
| Gene/Protein MultiSearch | YES | YES | |||
| Reaction MultiSearch | YES | YES | YES | ||
| Advanced Search | YES | YES | |||
| Comparative Analysis | YES | YES | YES |
1
This tool is being phased out.