WikiPathways protocols

View WikiPathways computational protocol

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WikiPathways specifications


Unique identifier OMICS_09773
Name WikiPathways
Software type Application/Script
Interface Web user interface, Application programming interface
Restrictions to use None
Computer skills Basic
Stability Beta
Maintained Yes


  • person_outline Marti Kutmon <>
  • person_outline Egon Willighagen <>

Publications for WikiPathways

WikiPathways in pipelines

PMCID: 5768180
PMID: 29367853
DOI: 10.3389/fimmu.2017.01938

[…] homer uses a one-sided fisher’s exact test to determine the significance of over-representation of a gene set in the input list. we focused our analysis on enriched pathway gene sets from wikipathways () as it is the most comprehensive open source pathway collection. a more stringent cutoff of log2 fold-change ≥1 and fdr ≤ 0.001 was applied to select differentially expressed genes […]

PMCID: 5780744
PMID: 29363429
DOI: 10.1186/s12864-017-4339-5

[…] 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) cellular biomarkers (biomarkers). […]

PMCID: 5796402
PMID: 29390967
DOI: 10.1186/s12859-018-2041-5

[…] wanted to obtain genes which the variant might affect as well as available drugs targeting these affected genes, he would have to query multiple biothings apis, e.g. which contains wikipathways information, which contains variant annotation information, as well as which contains drug annotation information. thus, a typical workflow would involve […]

PMCID: 5796402
PMID: 29390967
DOI: 10.1186/s12859-018-2041-5

[…] “4633”.parse the annotation objects to get the wikipathways [] ids related to each gene from the field.query again to retrieve annotation objects related to the wikipathways ids from step d.parse the query results to retrieve all uniprot ids related to these wikipathways ids.query to retrieve the drug objects associated to the target proteins, […]

PMCID: 5802208
PMID: 29328449
DOI: 10.3892/mmr.2018.8385

[…] for significance., the toppgene database ( () integrates pathway information in biosystems [including biocyc, kyoto encyclopedia of genes and genomes (kegg), reactome, wikipathways], genmapp, msigdb c2 (including biocarta, sigmaaldrich and signaling gateway), pantherdb, pathway ontology and small molecule pathway database databases, and can be used for functional […]

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WikiPathways in publications

PMCID: 5939684
DOI: 10.1167/iovs.18-24091

[…] 2.2.3) and analysis of biological pathways based on the database for annotation, visualization and integrated discovery (david, available in the public domain, and wikipathways (available in the public domain, to identify biological processes affected by mirna dysregulation., expression levels of de mirnas and inversely expressed mrnas […]

PMCID: 5916929
PMID: 29695774
DOI: 10.1038/s41467-018-03766-z

[…] with random forests in fig.  (training on cohort1 qpcr data and evaluating on the independent cohort 2 qpcr data). for additional power, each sample was scored using a database of curated pathways ( briefly, for each patient, we computed pathway expression scores, based on the sum of overlapping genes in each pathway and the qpcr data. from the 569 original pathways […]

PMCID: 5906971
PMID: 29760827
DOI: 10.2174/1874364101812010041

[…] was performed using toppgene ( additional databases utilized included: kyoto encyclopedia of genes and genomes (, wikipathways (, reactome (, comparative toxicogenomics database (, stitch (, and broad institute connectivity map […]

PMCID: 5884322
PMID: 29438851
DOI: 10.1016/j.jprot.2018.02.015

[…] using volcano plots using log2 (fold change) plotted against significance in r studio. pathway analysis of label free quantitative proteomic data was performed using pathvisio [] together with wikipathways [] to visualize and highlight altered pathways from identified proteins., in these experimental conditions we considered cys containing peptides that were identified as labelled […]

PMCID: 5908973
PMID: 29706885
DOI: 10.3389/fnagi.2018.00102

[…] in graphpad prism (rrid:scr_002798, v7.00) with a level of statistical significance set at p < 0.05., gene ontology (go) annotations and significantly altered pathways in kegg, reactome, and wikipathways were analyzed using genetrail2 (; rrid:scr_006250, v1.5; go, kegg, reactome retrieved 11/01/2016; wikipathways retrieved 18/02/2016) with the gene set enrichment analysis (gsea) method. […]

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WikiPathways institution(s)
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands; Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, The Netherlands; Gladstone Institutes, San Francisco, CA, USA; University of Vienna, Department of Pharmaceutical Chemistry, Vienna, Austria; Chair of Nutritional Physiology, Technische Universitat Munchen, Freising, Germany; Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, Suita, Osaka, Japan; Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA; Micelio, Antwerp, Belgium; School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands
WikiPathways funding source(s)
Supported by Innovative Medicines Initiative Joint Undertaking [115191]; National Institutes of Health [GM100039]; Google Summer of Code; National Cancer Institute [U24- CA210954]; Dutch Province of Limburg; and Netherlands Organisation for Scientific Research [21002-NWO-ODEX 650.002.002].

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