KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data.

Authors:
Nozomu Sakurai
Nozomu Sakurai
Kazusa DNA Research Institute
Japan
Takeshi Ara
Takeshi Ara
Kazusa DNA Research Institute
Yoshiyuki Ogata
Yoshiyuki Ogata
Kazusa DNA Research Institute
Japan
Ryosuke Sano
Ryosuke Sano
Graduate School of Science
Japan
Takashi Ohno
Takashi Ohno
Tottori Prefectural Kousei Hospital
Kenjiro Sugiyama
Kenjiro Sugiyama
Graduate School of Agricultural Science
Kiyoshi Yamazaki
Kiyoshi Yamazaki
Mayo Clinic College of Medicine
Rochester | United States

Nucleic Acids Res 2011 Jan 19;39(Database issue):D677-84. Epub 2010 Nov 19.

Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan.

Correlations of gene-to-gene co-expression and metabolite-to-metabolite co-accumulation calculated from large amounts of transcriptome and metabolome data are useful for uncovering unknown functions of genes, functional diversities of gene family members and regulatory mechanisms of metabolic pathway flows. Many databases and tools are available to interpret quantitative transcriptome and metabolome data, but there are only limited ones that connect correlation data to biological knowledge and can be utilized to find biological significance of it. We report here a new metabolic pathway database, KaPPA-View4 (http://kpv.kazusa.or.jp/kpv4/), which is able to overlay gene-to-gene and/or metabolite-to-metabolite relationships as curves on a metabolic pathway map, or on a combination of up to four maps. This representation would help to discover, for example, novel functions of a transcription factor that regulates genes on a metabolic pathway. Pathway maps of the Kyoto Encyclopedia of Genes and Genomes (KEGG) and maps generated from their gene classifications are available at KaPPA-View4 KEGG version (http://kpv.kazusa.or.jp/kpv4-kegg/). At present, gene co-expression data from the databases ATTED-II, COXPRESdb, CoP and MiBASE for human, mouse, rat, Arabidopsis, rice, tomato and other plants are available.

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http://dx.doi.org/10.1093/nar/gkq989DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013809PMC

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January 2011
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References

(Supplied by CrossRef)
The prediction of local modular structures in a co-expression network based on gene expression datasets
Ogata et al.
Genome Inform. 2009
Current progress in computational metabolomics
Wishart et al.
Brief Bioinform. 2007

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