The plant-specific database. Classification of Arabidopsis proteins based on their phylogenetic profile.

One of the main goals of the plant community is to determine the function of every Arabidopsis gene by the end of the year 2010 (Chory et al., 2000). Because many are not yet characterized and because they will not be studied in other model organisms, we believe Arabidopsis proteins that are unique to the plant lineage should be a priority for future studies. Furthermore, functional characterization of plant-specific proteins is likely to provide novel insights about plant biology. In an effort to aid the functional characterization of the Arabidopsis proteins that are specific to plants, we have created the Plant-Specific Database (PLASdb). PLASdb contains Arabidopsis proteins classified according to their pattern of sequence similarity to proteins in organisms from all forms of life. PLASdb identifies 3,848 Arabidopsis proteins as plant specific because they are found only in plant species. In addition, 4,816 other proteins are classified in various groups based on their specific patterns of conservation among other Eukarya, Bacteria, or Archaea. The main goal of PLASdb is to stimulate further research on some of the least-studied proteins of plants. To this end, we have compiled and integrated information from public data sources (e.g. The Institute for Genomic Research [TIGR], Munich Information center for Protein Sequences [MIPS], The Arabidopsis Information Resource [TAIR]) with links to the original information and provided links to external databases (e.g. Salk Institute Genomic Analysis Laboratory [SIGNAL]). In addition, we have performed predictions of subcellular localization and transmembrane helices, analyzed gene expression in organs based on expressed sequence tag (EST) frequencies and microarray data, and grouped protein families based on sequence similarity clustering (BLASTCLUST). Web-based interfaces to several search engines allow gene-driven or exploratory modes of data access. Information in PLASdb can be quickly downloaded in text or Excel format for further analysis (http://genomics.msu.edu/plant_specific).