title: KEGGscape: a Cytoscape app for pathway data integration.
abstract: 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.
authors.affiliation: Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, Osaka, 565-0874, Japan ; JST, National Bioscience Database Center (NBDC), Tokyo, 102-0081, Japan.
authors.forename: Kozo
authors.initials: K
authors.lastname: Nishida
authors.affiliation: Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA.
authors.forename: Keiichiro
authors.initials: K
authors.lastname: Ono
authors.affiliation: Graduate School of Information Science, Nara Institute of Science and Technology, Nara, 630-0101, Japan.
authors.forename: Shigehiko
authors.initials: S
authors.lastname: Kanaya
authors.affiliation: Laboratory for Biochemical Simulation, RIKEN Quantitative Biology Center, Osaka, 565-0874, Japan.
authors.forename: Koichi
authors.initials: K
authors.lastname: Takahashi