Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/7/2007
Publication Date: 12/7/2007
Citation: Cannon, E.K., Dash, S., Lu, H., Nadkarni, D., Thomas, A., Lauter, N.C., Brendel, V., Wise, R.P., Dickerson, J.A. 2007. PLEXdb: Plant and Pathogen Expression Database and Tools for Comparative and Functional Genomics Analysis [abstract]. Annual International Plant & Animal Genome Conference. Abstract Book. p. 351.
Technical Abstract: PLEXdb is a plant expression database that supports all Affymetrix microarray designs for plants and plant pathogens. PLEXdb provides annotation and hand-curated microarray data. Experiments deposited in PLEXdb are checked for MIAME/Plant compliance and completeness, then processed by normalizing the raw data using RMA and MAS5.0, producing tables and graphics from the resulting data. Experiment data, both raw and normalized, may be explored online and can be downloaded. PLEXdb provides graphical visualizations of raw and normalized data across treatments in the form of boxplots, heatmaps, dendrograms, scatterplots, and quality control plots. Expression levels of individual or sets of genes can be investigated via fold change plots, groupings of similarly expressed genes, and expression graphs. Experiment data may be designated as private, shared with a group of collaborators and reviewers, or made visible to the public. This enables researchers to use PLEXdb at any stage of their data analysis. PLEXdb tools such as the Microarray Platform Translator and the Model Genome Interrogator allow users to search for homologous genes on different microarray platforms and to translate microarray probes onto model genomes. PLEXdb uses standardized vocabularies such as the gene and plant ontologies to improve searching and cross-experiment comparisons. Links to plant and pathogen databases such as PlantGDB, Gramene, GrainGenes, MIPS Fusarium graminearum Genome Database, and UniProt provide detailed sequence data and annotation.