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KATSURA: KEGG PATHWAY COVERAGE AND EXPRESSION ANALYSIS

The Katsura tool is a free open source Java application designed to overlay gene expression data, comparative genomics data, or quantitative shotgun proteomics data onto metabolic pathways. Katsura uses data from the Kyoto Encyclopedia of Genes and Genomes (KEGG, 1-3), Kanehisa Laboratory at Kyoto University, to build a small database containing KEGG pathway and enzyme data relating to one or more user specified organisms. Katsura manages the local database allowing users to update core information, add genomes of interest, backup the database and display database status reports. Gene expression data is input to allow visualization of pathway level expression trends over time or over a series of experimental conditions. A separate table visualizes the individual enzymes and associated gene expression values for each pathway. Capabilities such as bookmarking pathways to annotate findings, saving results to reloadable files, and the ability to output pdf reports and summary files help to capture key research findings.

Features

  • A quick-start tutorial and dataset clearly illustrates the main functions of the tool
  • Full support for database creation, customization, and management
  • User selected resources are downloaded and loaded into the database automatically
  • Pathway and enzymes are organized by pathway category for structured browsing
  • Expression or CGH-based queries display pathway expression or coverage
  • Utility database queries allow comparison of multiple genome annotations
  • Pathway and component enzyme expression graphs enhance trend visualization

Download Version 1.0

Click here for application: Download Application

This application is released under the GPL v3. License: View License

Click here for service pack: Download Service Pack

Click here for source code: Download Source Code

Software Manual

The Katsura Manual contains a complete description of its capabilities and a description of how the tool is used. The manual also includes information on the KEGG resources and the small H2 database. Please view the manual to learn more about Katsura’s capabilities.

View Manual

System Requirements

  • Operating Systems: Windows XP/Vista/7, Linux, Mac OSX 10.4 or greater.
  • Memory Requirement (RAM): 1 GB recommended, 512MB is adequate.
  • Java Runtime Environment (JRE): Version 1.5 or greater.

Download Java v1.6.0

Contact

The developers of the Katsura tool encourage questions on the use of the tool and constructive comments or ideas for future enhancements.

Contact the PFGRC's Katsura Development Team by email: katsura@jcvi.org

References

  1. Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M., and Hirakawa, M.; KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355-D360 (2010).
  2. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M.; From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354-357 (2006).
  3. Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).
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