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Table 2 Comparison of resources with SignaLink 2

From: SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks

 

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

 

  1. 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.