|Comparison of resources with SignaLink 2|
|KEGG||Reactome||SPIKE||ConsensusPathDB||TranscriptomeBrowser||SignaLink 1||SignaLink 2|
|Contains integrated data||√||√||√|
|Reference for each interaction||√||√||√||√|
|Cross-talks and multi-pathway proteins*||√||√||√|
|Undirected protein-protein interactions||√||√||√||√||√|
|Directed protein-protein interactions†||√||√|
|Transcription factor regulation||√||√||√||√|
|Transcription factors that regulate miRNAs||√|
|Confidence score for the interactions||√|
|Customizable download options||√ˣ||√||√|
|Freely downloadable for academic users||√||√||√||√||√||√|
We compared the major features of SignaLink 2 with three pathway databases (KEGG, Reactome and SPIKE), an integrated pathway resource, ConsensusPathDB, and an integrated regulatory resource, TranscriptomeBrowser. We also compared the features of SignaLink 2 with its previous version to show the major upgrade and extension. #Only those species were taken into account that were represented with experimental data in the resource (i.e., orthology derived predictions were not considered). § Manual curation performed by the developers of the resource (i.e., not integrated from external resources). * All types of cross-talks (transcriptional, post-transcriptional and post-translational) were taken into account but only in those cases where the structure of the resource allowed to easily download cross-talks and multi-pathway proteins (i.e., without any computational evaluation). † Only protein-protein interactions (PPIs) with predicted directions were taken into account. ˣ Only available with the InteractomeBrowser plugin.
Fazekas et al.
Fazekas et al. BMC Systems Biology 2013 7:7 doi:10.1186/1752-0509-7-7