Submitted to: International Triticeae Mapping Initiative Workshop
Publication Type: Proceedings
Publication Acceptance Date: 4/28/2005
Publication Date: 5/30/2005
Citation: Wise, R.P., Shen, L., Gong, J., Xin, J., Caldo, R., Nettleton, D., Dickerson, J. 2005. BarleyBase/WheatPLEX: The triticeae hub of PLEXdb plant expression database. International Triticeae Mapping Initiative Workshop. Available: http://wheat.pw.usda.gov/ITMI/ITMI2005/Wise_BarleyBase/.
Technical Abstract: PLEXdb (www.plexdb.org) is a unified public resource for large-scale Plant Expression data. With the advent of increasing amounts of DNA chips for many crop species, the long-term goal for PLEXdb is to make possible efficient access to highly parallel expression data with seamless portals to related genetic, physical, and trait data. Therefore, for each of the 400,000 microarray probe sets in PLEXdb, users will have “click-through” access to gene expression in multiple conditions, gene function annotations, genetic and physical map location by sequence-based alignments, and potential associations with trait data. Integral to this effort are BarleyBase and WheatPLEX - interlinked resources that house user contributed experiments from the Affymetrix 22K Barley1 and 61K Wheat GeneChips. Evolving from the BarleyBase expression database project, PLEXdb features MIAME-compliant experiment annotations as well as required Plant Ontology terms through PLEX Express, its user-friendly, web-based submission tool. Data will be linked to analytical and biological functions (e.g., BLAST, spliced alignment, multiple alignment, regulatory motif identification, and expression analysis). Use of plant and trait ontology terms allows cross-species comparisons based upon the common identifiers, facilitating interoperability between existing plant databases to determine genes that have similar expression profiles. PLEXdb will serve the community by integrating multiple data sets within and across species for comprehensive comparative genomics studies.