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Pathway Commons specifications


Unique identifier OMICS_02761
Name Pathway Commons
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Allowed
Version 2.0
Maintained Yes



  • person_outline Vcell Team

Publications for Pathway Commons

Pathway Commons citations


Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming

BMC Bioinformatics
PMCID: 5850944
PMID: 29536824
DOI: 10.1186/s12859-018-2034-4

[…] Even if the task of compiling signaling networks may be considered time demanding, many publicly available resources containing regulatory information currently exist such as KEGG [], Reactome [, ], Pathway Commons [], OmniPath [] and NDEX []. Some of these resources have available tools or Cytoscape [] plug-ins to extract networks given a list of molecules, such as ReactomeFIViz [] for Reactome, […]


Genetic heterogeneity of primary lesion and metastasis in small intestine neuroendocrine tumors

Sci Rep
PMCID: 5830878
PMID: 29491456
DOI: 10.1038/s41598-018-22115-0

[…] anker, which is based on FuncAssociate. For pathway analysis, gene associations with over 400 canonical signal transduction pathways were performed collected from the Pathway Interaction Database and pathway commons,. All canonical pathways are derived from Homo sapiens. Genes were grouped into non-synonymously mutated genes in primary lesions as well as in metastasis of SI-NETs. […]


RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites

PMCID: 5876005
PMID: 29470400
DOI: 10.3390/metabo8010016

[…] metabolic flux analysis. Of these, MetaboAnalyst 3.0 [], IMPaLA [], XCMS [,], and Metabox [] integrate metabolomics and gene expression for pathway enrichment and/or network analysis (). In addition, Pathway Commons [] integrates many sources of pathway annotations and includes functionalities for pathway analysis on genes (). While Metabox, XCMS, and MetaboAnalyst primarily use KEGG annotations, […]


A computationally driven analysis of the polyphenol protein interactome

Sci Rep
PMCID: 5797150
PMID: 29396566
DOI: 10.1038/s41598-018-20625-5
call_split See protocol

[…] the polyphenol list was searched in CHEBI database, containing ~100,000 entries, for corresponding CHEBI ID’s based on standardised SMILES. Polyphenol-protein interactions were mined from the STITCH, Pathway Commons and BindingDB databases, which collect information from multiple and often redundant databases, using name and CHEBI ID. Depending on the database, the term ‘interaction’ can either re […]


Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes

BMC Genomics
PMCID: 5780744
PMID: 29363429
DOI: 10.1186/s12864-017-4339-5
call_split See protocol

[…] tly changed. UCSC gene IDs were transformed into RefSeq IDs prior to GO-Elite analyses. GO-Elite uses 10 databases for identifying functional enrichments: (1) Gene Ontology, (2) Disease Ontology, (3) Pathway Commons, (4) GO Slim, (5) WikiPathways, (6) KEGG, (7) Transcription factor to target genes, (8) microRNA to target genes, (9) InterPro and UniProt functional regions (Domains), and (10) Cellul […]


The node weighted Steiner tree approach to identify elements of cancer related signaling pathways

BMC Bioinformatics
PMCID: 5751691
PMID: 29297291
DOI: 10.1186/s12859-017-1958-4

[…] on protein-protein interactions, such as BIND [], BioGRID [], DIP [], OPHID [] and String []. Similarly, there are many databases on signaling pathways, such as KEGG [], Reactome [], PANTHER [], and Pathway Commons []. Since String is one of the most comprehensible databases of protein-protein interactions (there are 2031 organisms, 9.6 million proteins, and 184 million protein-protein interactio […]


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Pathway Commons institution(s)
Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA; Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA; Banting and Best Department of Medical Research, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
Pathway Commons funding source(s)
National Institutes of Health, National Human Genome Research Institute (grant number P41HG004118); National Institute of General Medical Sciences (grant number 2R01GM070743-06); National Institute of General Medical Sciences Training Grant (grant number 1T32 GM083937); National Cancer Institute caBIG program

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