KAGIANA

Japanese version is here

Renewed at July 29, 2009; Updated at November 12,2008

Here is a portal site of the KAGIANA tool to retrieve genomic information and co-expressed genes in Arabidopsis.

Renewed using the TAIR9 dataset.

Gene Ontology data have been modified !

Interconnected to CoP (upgraded from CoexProcess)

Attention ! The 'Data' sheet has been reconstructed in the renewal. The direct links to public databases in the 'Selected_Link' sheet have been modified.

Download

• KAGIANA without macro programs (KAGIANA0906e.xls), released !



• KAGIANA with macro programs (KAGIANA0906m.xls), coming soon



• KAGIANA published in 2008 (KAGIANA0806.xls), using the TAIR8 dataset



• KAGIANA without macro programs in Japanese (KAGIANA0906j.xls), released !

The password to extract the ZIP files : nedo

For Macintosh users, it is recommended to use a software to uncompress a ZIP file with a password such as StuffIt Expander.

For Excel 2007 or later users, it is recommended to put this tool in a responsible folder to validate the macro programs for the following functions.

Available macro programs (coming soon for Windows users only)

• Retrieval of co-expressed genes using the Confeito algorithm for plant co-expression analysis
• Depiction of expression profiles of multiple genes
• Depiction of a pie chart of frequency of Gene Ontology terms
• Download of an expression profile of each gene from the ATTED-II database

Modifying macro programs

• Depiction of a co-expression network

The older versions are here.

Correlation data files

• Correlation coefficient of +0.4 or higher (54.7MB)
• Correlation coefficient of +0.5 or higher (21.7MB)
• Correlation coefficient of +0.6 or higher (8.5MB)
• Correlation coefficient of +0.7 or higher

Password for extraction of ZIP files : nedo

These correlation data are provided by Dr. Obayashi, the administrator of the ATTED-II.

Publication

• Bioinformatics tools to discover co-expressed genes in plants. Ogata, Y., Sakurai, N., Provart, N.J., Steinhauser, D., Krall, L. In The handbook of Plant Functional Genomics Concepts and Protocols, edited by Kahl, G. and Meksem, K. pp. 309-335, WILEY-VCH Verlag. GmbH & Co. KGaA, Weinheim (2008)



• KAGIANA: an Excel-based tool for retrieving summary information on Arabidopsis genes. Ogata, Y., Sakurai, N., Aoki, K., Suzuki, H., Okazaki, K., Saito, K., Shibata, D. Plant and Cell Physiology, 50(1):173-177 (2009)

Links

Plant co-expression

• ATTED-II for analyzing Arabidopsis co-expressed genes and predicting cis-elements



• The CoP for plant co-expressed biological processes, upgraded from CoexProcess



• The RnR for predicting the regulation of gene expression and metabolite accumulation in Arabidopsis T87 cultured cells

e-mail: yogata@kazusa.or.jp

Y. Ogata, Kazusa DNA Research Institute