Table 2 Comparison of salient features of NetPath with other popular curated signaling pathway resources
From: NetPath: a public resource of curated signal transduction pathways
Pathway resource | Query option for pathway molecules | Genes transcriptionally regulated by pathway included? | Pathways reviewed by experts? | File formats available for download | Textual description of reactions provided? | Other features or comments |
|---|---|---|---|---|---|---|
NetPath [5] | Yes | Yes | Yes | BioPAX, PSI-MI, SBML, Excel, Tab-delimited | Yes | Focus on human receptor mediated signaling. Also contains separate molecule pages with brief summary of the biology of the individual molecules |
BioCarta [14] | Yes | No | Yes | No download option provided | No | BioCarta provides commercial links to antibody reagents |
Science's STKE [15] | No | No | Yes | SVG | No | Contains species-specific and also cell-type-specific pathways |
KEGG [13] | Yes | No | No | KGML, BioPAX | No | Contains disease specific pathways |
Reactome [16] | Yes | No | Yes | BioPAX, SBML, PDF, SVG, Protégé, MySQL database dump | Yes | Also contains computationally inferred pathway reactions |
NCI-PID [17] | Yes | No | Yes | XML, BioPAX, SVG, JPG | No | Apart from NCI-Nature curated pathways, it also contains many pathways imported from BioCarta/Reactome |
CST [18] | Yes | No | Yes (in some cases) | No | Provides pathway information along with links to protein and commercial products available for that protein | |
WikiPathways [25] | Yes | No | No | GPML, GenMAPP, PDF, PNG, SVG | No | Any user can register and create a new pathway and also edit existing pathways |
PANTHER [26] | Yes | No | Reviewed by Curation Coordinator | SBML, SBGN, PNG | No | Allows community pathway curation and also provides links to Applied Biosystems genomic products |