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KEGGscape specifications


Unique identifier OMICS_08566
Name KEGGscape
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License Apache License version 2.0
Computer skills Medium
Version 0.7.0
Stability Stable
Maintained Yes


No version available


  • person_outline Kozo Nishida

Publication for KEGGscape

KEGGscape citations


Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis

PLoS One
PMCID: 5215829
PMID: 28056027
DOI: 10.1371/journal.pone.0168183

[…] roteins in the KEGG pathway maps and conduct a pathway enrichment analysis using a hypergeometric test. To visualize the pathways for publication, we used Cytoscape (v3.3.0, []) and the Cytoscape app KEGGscape (v0.7.0, []). […]


Uterine glands impact uterine receptivity, luminal fluid homeostasis and blastocyst implantation

Sci Rep
PMCID: 5131473
PMID: 27905495
DOI: 10.1038/srep38078
call_split See protocol

[…] tion of genes corresponding to those expression modules were assessed by mapping the genes to KEGG (Kyota Encyclopedia of Genes and Genomes) pathways as well GO (Gene Ontology) databases using tools (KEGGscape and BINGO) included in Cytoscape.Genes that were decreased or absent in PUGKO as compared to WT mice were further analyzed to predict gene functions, pathways and networks. Pathway analysis […]


Tools for visualization and analysis of molecular networks, pathways, and omics data

PMCID: 4461095
PMID: 26082651
DOI: 10.2147/AABC.S63534

[…] o clustering to pathway visualization and analysis. For instance, the Cytoscape plugins WikiPathways, and CyKEGGParser parse and visualize WikiPathways and KEGG pathways, respectively. KGMLReader and KEGGScape are plugins provided by KEGG for pathway import and visualization in Cytoscape versions 2 and 3, respectively. Similarly, the Reactome FI (Functional Interaction) plugin finds pathways and n […]


Cytoscape tools for the web age: D3.js and Cytoscape.js exporters

PMCID: 4264639
PMID: 25520778
DOI: 10.5256/f1000research.4824.r5313

[…] JSON files, and finally they can create custom web-based, interactive visualizations from the template projects ( ). The original network data visualized in was imported with a Cytoscape app called KEGGScape ( The advantage of this workflow is that users can use the large collection of existing Cytoscape apps for data integration and analysis, and the r […]


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KEGGscape institution(s)
Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, Osaka, Japan
KEGGscape funding source(s)
This work was supported by National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST).

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