WikiPathways statistics

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Citations per year

Number of citations per year for the bioinformatics software tool WikiPathways
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Tool usage distribution map

This map represents all the scientific publications referring to WikiPathways per scientific context
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Associated diseases

This word cloud represents WikiPathways usage per disease context
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Protocols

WikiPathways specifications

Information


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

Maintainers


  • person_outline Marti Kutmon
  • person_outline Egon Willighagen

Publications for WikiPathways

WikiPathways citations

 (164)
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New perspectives: systems medicine in cardiovascular disease

2018
BMC Syst Biol
PMCID: 5921396
PMID: 29699591
DOI: 10.1186/s12918-018-0579-5
call_split See protocol

[…] to biological pathway and interaction knowledge. The most prominent pathway databases are Reactome [], the Network Data Exchange (NDEx) [], the Kyoto Encyclopedia of Genes and Genomes (KEGG) [], and WikiPathways [] as well as disease-specific databases such as the Online Mendelian Inheritance in Man (OMIM) resource []. Databases focusing on molecular interactions include BioGRID [], IntAct [] and […]

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Pure flavonoid epicatechin and whole genome gene expression profiles in circulating immune cells in adults with elevated blood pressure: A randomised double blind, placebo controlled, crossover trial

2018
PLoS One
PMCID: 5908087
PMID: 29672527
DOI: 10.1371/journal.pone.0194229
call_split See protocol

[…] lue was <0.05. Changes in gene expression were related to changes in pathways by gene set enrichment analysis (GSEA) []. Gene sets were obtained from the KEGG, National Cancer Institute, Reactome and WikiPathways pathway databases. Only gene sets consisting of more than 10 and fewer than 500 genes were taken into account. The statistical significance of GSEA results was determined using 1,000 perm […]

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Transcriptome Analysis of Orbital Adipose Tissue in Active Thyroid Eye Disease Using Next Generation RNA Sequencing Technology

2018
PMCID: 5906971
PMID: 29760827
DOI: 10.2174/1874364101812010041
call_split See protocol

[…] sis was performed using ToppGene (https://toppgene.cchmc.org/enrichment.jsp). Additional databases utilized included: Kyoto Encyclopedia of Genes and Genomes (http://www.genome.jp/kegg/pathway.html), WikiPathways (www.wikipathways.org), Reactome (http://www.reactome.org), Comparative Toxicogenomics Database (http://ctdbase.org), STITCH (http://stitch.embl.de), and Broad Institute Connectivity Map […]

library_books

Redox responses are preserved across muscle fibres with differential susceptibility to aging

2018
J Proteomics
PMCID: 5884322
PMID: 29438851
DOI: 10.1016/j.jprot.2018.02.015

[…] alised 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. […]

library_books

Selection for growth rate and body size have altered the expression profiles of somatotropic axis genes in chickens

2018
PLoS One
PMCID: 5891002
PMID: 29630644
DOI: 10.1371/journal.pone.0195378

[…] oteins. However, the entire biological mechanism includes connections with several other signaling mechanisms as well []; http://sabiosciences.com/pathway.php?sn=Growth_Hormone_Signaling; https://www.wikipathways.org/index.php/Pathway:WP2657). The interested reader is referred to this review and the pathways databases.y, which is consistent with Both Chinese indigenous chicken breeds showed higher […]

library_books

From SNPs to pathways: Biological interpretation of type 2 diabetes (T2DM) genome wide association study (GWAS) results

2018
PLoS One
PMCID: 5884486
PMID: 29617380
DOI: 10.1371/journal.pone.0193515

[…] We used GOElite [] to provide a biological description from the Gene Ontology for the 678 genes that were not found in the complete WikiPathways curated collection, and therefore not represented in the SNP-gene-pathway network. When we used all three main GO classes, molecular function, biological process and cellular component, 6 […]


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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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