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.

Figure 1.

General workflow for analysis of metabolic pathways using the KaPPA-View tool. A user sends a CSV-formatted dataset of transcripts and/or metabolites from their personal computer (PC) to the Web server through the Internet. The application engine (KV-Engine) processes the data and interacts with the pathway information library. The SVG-formatted files generated by the engine are returned to the user's PC through the Adobe SVG Viewer installed on the PC. Users also can access the transcript and metabolite data library located on the KaPPA-View server.

Figure 2.

Symbolic representation of enzymatic reactions and transcripts on the metabolic pathway maps. A, Diagrammatic representation of an enzymatic reaction with substrate and the reaction product represented by circles, an arrow representing the reaction, and squares for the transcripts involved, or putatively assigned to be involved, in the reaction. Names for the substrate, product, and enzyme encoded by transcripts are also given. The colors of the symbols change according to quantitative data of either transcripts or metabolites. B, The color charts for defining quantitative data for transcripts (left) and metabolites (right). C, Three color levels for pathway maps, subclass, and metabolism category for transcripts (T) and metabolites (M). The numbers of either transcripts or metabolites analyzed by the dataset (xxx) and listed on the metabolic pathway map (yyy) are also indicated to the left of the pathway indicators.

Figure 3.

Pop-up windows for displaying information on the metabolic pathway maps. A to C, The element list containing all of the information available for the elements (the reaction, genes involved, and metabolites) on the map being displayed on the user's browser (A), the metabolite reference page (B), and the enzyme reference page (C). The gene reference page (not shown) can also be chosen from the element lists.

Figure 4.

Representation of the transcript and metabolite dataset for wild type and PAP1-overexpressing plants. The dataset for wild-type and transgenic plants (Tohge et al., 2005) were displayed on the metabolic pathway maps for flavonoids (A) and anthocyanins (B) and the bird's-eye map (C). The changes in individual transcripts and metabolites on the map are shown as squares and circles with different colors matched using the color charts (D and E). The changes in the transcripts for glycosyltransferase (F) and acyltransferase (G) are shown.

Figure 5.

Data components of the MySQL-KaPPA-View tool.