NAR Molecular Biology Database Collection entry number 880
Toyoda T. and Mochizuki Y.
Phenome Informatics Team, Functional Genomics Research Team, Genomic Sciences Center, RIKEN, 1-7-22, Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
The tiling array is a powerful tool to discover the unknown transcripts that were essentially undetectable by construction of cDNA libraries or by strictly sequence-based gene predictions. Here we introduce a database named ARTADEdb containing transcriptional structures elucidated by our original statistical method ARTADE which estimates exon/intron structures of structurally unknown genes based on both tiling array data and genomic sequence data. By applying it to genome-wide tiling array data from four tissues in Arabidopsis, 14,782 transcriptional units (TUs) including 5,250 novel TUs found in the intergenic regions were registered in ARTADEdb. As 84.4% of the novel TUs were verified to be actually expressed by comparison with Arabidopsis UniGene clusters, the results are of benefit for researchers hunting for novel genes and their functions. The predicted genes were annotated with information on their expression values, significances of the expressions, nucleic- and amio-acid sequences, functionally known references, and were clustered as TUs based on their genomic positions. For the userâ€™s convenience, the gene records are related to available mutants, full-length cDNAs, literature-based related genes, and ontologies. In the database system, the genes can be searched by specifying keywords related to the above-mentioned annotations, filtered by expression cutoffs or other criteria, and the resulting list is ranked based on various parameters. The system also supplies a primer-designing function so that promising candidate genes are quickly verified experimentally. The database is integrated in our original data-retrieval framework named GPS: Genome?Phenome Superhighway, and is accessible at http://omicspace.riken.jp/ARTADE/.
Category: Nucleotide Sequence Databases
Subcategory: Gene structure, introns and exons, splice sites
Category: Plant databases
Subcategory: Arabidopsis thaliana
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