title: KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps.
abstract: The application of DNA array technology and chromatographic separation techniques coupled with mass spectrometry to transcriptomic and metabolomic analyses in plants has resulted in the generation of considerable quantitative data related to transcription and metabolism. The integration of "omic" data is one of the major concerns associated with research into identifying gene function. Thus, we developed a Web-based tool, KaPPA-View, for representing quantitative data for individual transcripts and/or metabolites on plant metabolic pathway maps. We prepared a set of comprehensive metabolic pathway maps for Arabidopsis (Arabidopsis thaliana) and depicted these graphically in Scalable Vector Graphics format. Individual transcripts assigned to a reaction are represented symbolically together with the symbols of the reaction and metabolites on metabolic pathway maps. Using quantitative values for transcripts and/or metabolites submitted by the user as Comma Separated Value-formatted text through the Internet, the KaPPA-View server inserts colored symbols corresponding to a defined metabolic process at that site on the maps and returns them to the user's browser. The server also provides information on transcripts and metabolites in pop-up windows. To demonstrate the process, we describe the dataset obtained for transgenic plants that overexpress the PAP1 gene encoding a MYB transcription factor on metabolic pathway maps. The presentation of data in this manner is useful for viewing metabolic data in a way that facilitates the discussion of gene function.
authors: Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan.
authors: Toshiaki
authors: T
authors: Tokimatsu
authors: Nozomu
authors: N
authors: Sakurai
authors: Hideyuki
authors: H
authors: Suzuki
authors: Hiroyuki
authors: H
authors: Ohta
authors: Kazuhiko
authors: K
authors: Nishitani
authors: Tanetoshi
authors: T
authors: Koyama
authors: Toshiaki
authors: T
authors: Umezawa
authors: Norihiko
authors: N
authors: Misawa
authors: Kazuki
authors: K
authors: Saito
authors: Daisuke
authors: D
authors: Shibata
mesh_terms: D019295:Computational Biology / Q000379:methods* / Q000639:trends; D003196:Computer Graphics; D018744:DNA, Plant / Q000235:genetics; D030541:Databases, Genetic; D017343:Genes, Plant; D018745:Genome, Plant; D016247:Information Storage and Retrieval; D020411:Oligonucleotide Array Sequence Analysis; D000073718:Pancreatitis-Associated Proteins; D018521:Plant Physiological Phenomena; D010944:Plants / Q000235:genetics* / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D018744:DNA, Plant; D000073718:Pancreatitis-Associated Proteins; C000612141:REG3A protein, human