KEGGscape: a Cytoscape app for pathway data integration

In this paper, we present KEGGscape a pathway data integration and visualization app for Cytoscape ( http://apps.cytoscape.org/apps/keggscape). KEGG is a comprehensive public biological database that contains large collection of human curated pathways. KEGGscape utilizes the database to reproduce th...

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Main Authors:	Nishida, Kozo, Ono, Keiichiro, Kanaya, Shigehiko, Takahashi, Koichi
Format:	Online
Language:	English
Published:	F1000Research 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4141640/

id	pubmed-4141640
recordtype	oai_dc
spelling	pubmed-41416402014-08-28 KEGGscape: a Cytoscape app for pathway data integration Nishida, Kozo Ono, Keiichiro Kanaya, Shigehiko Takahashi, Koichi Software Tool In this paper, we present KEGGscape a pathway data integration and visualization app for Cytoscape ( http://apps.cytoscape.org/apps/keggscape). KEGG is a comprehensive public biological database that contains large collection of human curated pathways. KEGGscape utilizes the database to reproduce the corresponding hand-drawn pathway diagrams with as much detail as possible in Cytoscape. Further, it allows users to import pathway data sets to visualize biologist-friendly diagrams using the Cytoscape core visualization function (Visual Style) and the ability to perform pathway analysis with a variety of Cytoscape apps. From the analyzed data, users can create complex and interactive visualizations which cannot be done in the KEGG PATHWAY web application. Experimental data with Affymetrix E. coli chips are used as an example to demonstrate how users can integrate pathways, annotations, and experimental data sets to create complex visualizations that clarify biological systems using KEGGscape and other Cytoscape apps. F1000Research 2014-07-01 /pmc/articles/PMC4141640/ /pubmed/25177485 http://dx.doi.org/10.12688/f1000research.4524.1 Text en Copyright: © 2014 Nishida K et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. http://creativecommons.org/publicdomain/zero/1.0/ Data associated with the article are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication).
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Nishida, Kozo Ono, Keiichiro Kanaya, Shigehiko Takahashi, Koichi
spellingShingle	Nishida, Kozo Ono, Keiichiro Kanaya, Shigehiko Takahashi, Koichi KEGGscape: a Cytoscape app for pathway data integration
author_facet	Nishida, Kozo Ono, Keiichiro Kanaya, Shigehiko Takahashi, Koichi
author_sort	Nishida, Kozo
title	KEGGscape: a Cytoscape app for pathway data integration
title_short	KEGGscape: a Cytoscape app for pathway data integration
title_full	KEGGscape: a Cytoscape app for pathway data integration
title_fullStr	KEGGscape: a Cytoscape app for pathway data integration
title_full_unstemmed	KEGGscape: a Cytoscape app for pathway data integration
title_sort	keggscape: a cytoscape app for pathway data integration
description	In this paper, we present KEGGscape a pathway data integration and visualization app for Cytoscape ( http://apps.cytoscape.org/apps/keggscape). KEGG is a comprehensive public biological database that contains large collection of human curated pathways. KEGGscape utilizes the database to reproduce the corresponding hand-drawn pathway diagrams with as much detail as possible in Cytoscape. Further, it allows users to import pathway data sets to visualize biologist-friendly diagrams using the Cytoscape core visualization function (Visual Style) and the ability to perform pathway analysis with a variety of Cytoscape apps. From the analyzed data, users can create complex and interactive visualizations which cannot be done in the KEGG PATHWAY web application. Experimental data with Affymetrix E. coli chips are used as an example to demonstrate how users can integrate pathways, annotations, and experimental data sets to create complex visualizations that clarify biological systems using KEGGscape and other Cytoscape apps.
publisher	F1000Research
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4141640/
_version_	1613126744733122560

KEGGscape: a Cytoscape app for pathway data integration

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