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Table 2 List of highly cited pathway databases for proteomic applications

From: Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development

Most cited repositories for biological pathways
Pathway databases Biological pathway Website/Link
Reactome KnowledgeBase Signal Transduction Pathway http://www.reactome.org
BioCarta Pathway Diagrams Signal Transduction Pathway http://www.biocarta.com/genes/index.asp
Pathway Commons Signal Transduction Pathway http://www.pathwaycommons.org/pc/
Protein ANalysis THrough Evolutionary Relationships Signal Transduction Pathway http://www.pantherdb.org
Protein Lounge Signal Transduction Pathway http://www.proteinlounge.com
WikiPathways Signal Transduction Pathway http://wikipathways.org/
Transcription Factor encyclopedia Regulatory Pathways http://www.cisreg.ca/cgi-bin/tfe/home.pl
Transcription Regulatory Regions Database Regulatory Pathways http://wwwmgs.bionet.nsc.ru/mgs/gnw/trrd/
A Public Database of Transcription Factor and Regulatory Sequence Annotation Regulatory Pathways http://www.pazar.info/
Homo Sapiens Comprehensive Model Collection (HOCOMOCO) Regulatory Pathways http://autosome.ru/HOCOMOCO/index.php
Transcription Factor Database Regulatory Pathways http://www.gene-regulation.com/index2.html
Human Protein Reference Database Protein-Protein Interactions http://www.hprd.org/
Human Annotated and Predicted Protein Interaction Database Protein-Protein Interactions http://bio.informatics.iupui.edu/HAPPI/
Biomolecular Interaction Network Database Protein-Protein Interactions http://bond.unleashedinformatics.com/
Molecular Interaction Database Protein-Protein Interactions http://mint.bio.uniroma2.it/mint/
Biological General Repository for Interaction Datasets Protein-Protein Interactions http://thebiogrid.org/
Search Tool for the Retrieval of Interacting Genes/Proteins Protein-Protein Interactions http://string.embl.de/