KaPPA-View4: A Pathway Database for Gene Co-expression and Metabolite Co-accumulation Analysis

Abstract

Correlations of gene-to-gene co-expression and metabolite-to-metabolite co-accumulation are considered to be useful for uncovering unknown functions of genes and regulatory systems of the metabolic pathways. Although many databases and tools are available to interpret quantitative data of transcriptome and metabolome, there are only limited ones that connect correlation data to biological knowledge and can be utilized to find biological significance of it. We developed a new metabolic pathway database, KaPPA-View4 ("http://kpv.kazusa.or.jp/kpv4/":http://kpv.kazusa.or.jp/kpv4/), that enables to overlay gene-to-gene and/or metabolite-to-metabolite relationships as quadratic Bezíer curves on metabolic pathway maps. For up to 4 maps including pathway maps, gene category maps, and user created maps can be analyzed on a single browser window, the 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 ("http://kpv.kazusa.or.jp/kpv4-kegg/":http://kpv.kazusa.or.jp/kpv4-kegg/). One of the major advanteges of utilizing KEGG pathway maps is that we can share the latest results of KEGG's continuous effort for curation of gene descriptions, categorizations, and assignment on the maps for various organisms. We currently provide pathway map data for 20 species including animals, plants and microorganisms, and gene co-expression data for 12 species that are retrieved from ATTED-II, COXPRESdb, CoP and MiBase.This work was supported by the New Energy and Industrial Technology Development Organization (NEDO, Japan).