Table 2

Comparison of resources with SignaLink 2
KEGG[71] Reactome[72] SPIKE[73] ConsensusPathDB[74] TranscriptomeBrowser[10] SignaLink 1[1] SignaLink 2
Model species#
Containsmanual curation§
Contains integrated data
Reference for each interaction
Cross-talks and multi-pathway proteins*
Undirected protein-protein interactions
Directed protein-protein interactions
Transcription factor regulation
miRNA 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

Open Data