Poster: Genomic & proteomic resources
Abs #
876: Arabidopsis microarray resources at TAIR
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Presenter: |
Moseyko, Nick , nickm@acoma.stanford.edu |
Authors | Moseyko, Nick (A) Garcia-Hernandez, Margarita (A) Zhang, Jessie (A) Miller, Neil (B) Montoya, Mary (B) Weems, Dan (B) Rhee, Sue (A) | | Affiliations: |
(A): Carnegie Institution of Washington
(B): National Center for Genome Resources
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| Web Site: | http://www.arabidopsis.org | |
The Arabidopsis Information Resource (TAIR) at arabidopsis.org has developed a database for Arabidopsis microarray data from both spotted microarrays and Affymetrix chips. The database conforms to established standards for publication of microarray data (MAIME). Data is primarily from large-scale projects, such as the Arabidopsis Functional Genomics Consortium (USA), NASC Arrays (UK), AtGenExpress (Germany), and the Compendium of Arabidopsis Gene Expression (Belgium). TAIR established an XML-based data sharing mechanism with ArrayExpress database in UK. Individual researchers are encouraged to submit their data using simple, pre-filled Excel spreadsheets (arabidopsis.org/info/microarray.submission.jsp). Extensive data curation, annotation, quality control and normalization procedures performed at TAIR make it possible to compare and analyze the results of many microarray experiments stored in the database. Besides raw and normalized data, TAIR provides arithmetic mean, standard error and other related statistical measures of gene expression for each gene from replicated spots per array (if available), replicated hybridizations (if available), and across all arrays. ANOVA calculations are included as a measure of whole array data quality. Researchers can search for data using several parameters, including experimental variables, experiment categories, plant tissue, and expression level. Raw data, normalized results, and clustered data are available for download. TAIR has on-line tools and stand-alone programs for searching and analyzing the data, and provides continual updates to the genome mapping of the publicly available array designs (e.g., AFGC, Affymetrix 8K, and Affymetrix 25K).
