title: KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data.
abstract: 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.
authors.affiliation: Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan. sakurai@kazusa.or.jp
authors.forename: Nozomu
authors.initials: N
authors.lastname: Sakurai
authors.forename: Takeshi
authors.initials: T
authors.lastname: Ara
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Ogata
authors.forename: Ryosuke
authors.initials: R
authors.lastname: Sano
authors.forename: Takashi
authors.initials: T
authors.lastname: Ohno
authors.forename: Kenjiro
authors.initials: K
authors.lastname: Sugiyama
authors.forename: Atsushi
authors.initials: A
authors.lastname: Hiruta
authors.forename: Kiyoshi
authors.initials: K
authors.lastname: Yamazaki
authors.forename: Kentaro
authors.initials: K
authors.lastname: Yano
authors.forename: Koh
authors.initials: K
authors.lastname: Aoki
authors.forename: Asaph
authors.initials: A
authors.lastname: Aharoni
authors.forename: Kazuki
authors.initials: K
authors.lastname: Hamada
authors.forename: Koji
authors.initials: K
authors.lastname: Yokoyama
authors.forename: Shingo
authors.initials: S
authors.lastname: Kawamura
authors.forename: Hirofumi
authors.initials: H
authors.lastname: Otsuka
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Tokimatsu
authors.forename: Minoru
authors.initials: M
authors.lastname: Kanehisa
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Suzuki
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
authors.forename: Daisuke
authors.initials: D
authors.lastname: Shibata
mesh_terms: D000818:Animals; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D006801:Humans; D020407:Internet; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D055442:Metabolome / Q000235:genetics*; D051379:Mice; D051381:Rats