KEGGscape specifications

Information


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
Requirements
Cytoscape
Maintained Yes

Versioning


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Maintainer


  • person_outline Kozo Nishida <>

Publication for KEGGscape

KEGGscape in publications

 (8)
PMCID: 5719083
PMID: 29213115
DOI: 10.1038/s41598-017-17000-1

[…] were then analyzed in cytoscape and the reactome fiviz app. groupings of metabolic genes were overlaid onto the kegg metabolic pathway through the online web portal and through cytoscape using keggscape to read in kegg kgml files for a given pathway. groupings of a. fumigatus differentially expressed genes based on normalized counts were analyzed for enrichment (hypergeometric test, […]

PMCID: 5405090
PMID: 28479747
DOI: 10.6026/97320630013025

[…] with e. coli k-12 using the cross referencing tool at ecogene []. the gene regulation information was downloaded from regulondb [] and the metabolic pathway information was downloaded from keggscape []. further cross referencing data was downloaded using annotationhub []., we propose a gene expression regulation analysis approach to detect the times at which gene expression regulators […]

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

[…] 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, [])., during the whole experiment, the strain p. malhamensis ds showed a more agitated movement and higher cell numbers in the light treatments. from a starting value […]

PMCID: 5131473
PMID: 27905495
DOI: 10.1038/srep38078

[…] 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 […]

PMCID: 5037646
PMID: 27708692
DOI: 10.1186/s13020-016-0112-y

[…] represent their relationships and are marked with two types of lines. the related diseases are marked with different colors at the nodes. the targeted diseases pathway was mapped using the keggscape plugin of cytoscape, version 3.2.tableĀ 3 aall drug information was obtained from ipa analysis and drugbank, aall drug information was obtained from ipa analysis and drugbank, in modern […]


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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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