title: DBATE: database of alternative transcripts expression.
abstract: The use of high-throughput RNA sequencing technology (RNA-seq) allows whole transcriptome analysis, providing an unbiased and unabridged view of alternative transcript expression. Coupling splicing variant-specific expression with its functional inference is still an open and difficult issue for which we created the DataBase of Alternative Transcripts Expression (DBATE), a web-based repository storing expression values and functional annotation of alternative splicing variants. We processed 13 large RNA-seq panels from human healthy tissues and in disease conditions, reporting expression levels and functional annotations gathered and integrated from different sources for each splicing variant, using a variant-specific annotation transfer pipeline. The possibility to perform complex queries by cross-referencing different functional annotations permits the retrieval of desired subsets of splicing variant expression values that can be visualized in several ways, from simple to more informative. DBATE is intended as a novel tool to help appreciate how, and possibly why, the transcriptome expression is shaped. DATABASE URL: http://bioinformatica.uniroma2.it/DBATE/.
authors.affiliation: Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica s.n.c., Rome 00133, Italy.
authors.forename: Valerio
authors.initials: V
authors.lastname: Bianchi
authors.forename: Alessio
authors.initials: A
authors.lastname: Colantoni
authors.forename: Alberto
authors.initials: A
authors.lastname: Calderone
authors.forename: Gabriele
authors.initials: G
authors.lastname: Ausiello
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Ferrè
authors.forename: Manuela
authors.initials: M
authors.lastname: Helmer-Citterich
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D030541:Databases, Genetic; D006801:Humans; D020407:Internet; D058977:Molecular Sequence Annotation; D060066:Protein Interaction Maps / Q000235:genetics; D057386:Search Engine; D014584:User-Computer Interface