Abstract
The Soybean Proteome Database (SPD) was created to provide a data repository for functional analyses of soybean responses to flooding stress, thought to be a major constraint for establishment and production of this plant. Since the last publication of the SPD, we thoroughly enhanced the contents of database, particularly protein samples and their annotations from several organelles. The current release contains 23 reference maps of soybean (Glycine max cv. Enrei) proteins collected from several organs, tissues, and organelles including the maps for plasma membrane, cell wall, chloroplast, and mitochondrion, which were analyzed by two-dimensional polyacrylamide gels. Furthermore, the proteins analyzed with gel-free proteomics technique have been added and are available online. In addition to protein fluctuations under flooding, those of salt and drought stress have been included in the current release. A case analysis employing a portion of those newly released data was conducted, and the results will be shown. An ‘omics table has also been provided to reveal relationships among mRNAs, proteins, and metabolites with a unified temporal-profile tag in order to facilitate retrieval of the data based on the temporal profiles. An intuitive user interface based on dynamic HTML enables users to browse the network as well as the profiles of the multiple “omes” in an integrated fashion. The SPD is available at: http://proteome.dc.affrc.go.jp/Soybean/
Highlights
One of the most advantageous uses of proteomic technology is the direct determination of biologically reacting proteins within a living organism
Proteome analysis linked to genome sequence information will be very useful for functional genomics in order to define the function of their associated genes from another aspect
With the aim of building the comprehensive platform for future soybean proteomics, we developed the Soybean Proteome Database (SPD, Sakata et al, 2009), which consists of the proteome data collected from plants in flooding stress conditions
Summary
One of the most advantageous uses of proteomic technology is the direct determination of biologically reacting proteins within a living organism. The agricultural legume soybean has been one of the most important crops in many countries For this crop plant, flooding stress is one of the natural conditions that exhibit a severe negative influence on the productivity of arable farmland (Komatsu et al, 2012). Includes multiple levels of biological data, transcriptome and metabolome in addition to the proteome Such integrated “omes” are coordinated as temporal profiles in which each element differentially expressed under flooding stress is compared to a control condition. The data from different “omes” are associated with each other based on manual annotations These features discriminate the SPD from other soybean databases, the Proteomics of Oilseeds (Hajduch et al, 2005) which stores data of seed filling stage from Glycine max cv. We will showcase an analysis of “comparative proteomics” with datasets comprising organs and subcellular compartments
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