title: OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica.
abstract: We report the development of OikoBase (http://oikoarrays.biology.uiowa.edu/Oiko/), a tiling array-based genome browser resource for Oikopleura dioica, a metazoan belonging to the urochordates, the closest extant group to vertebrates. OikoBase facilitates retrieval and mining of a variety of useful genomics information. First, it includes a genome browser which interrogates 1260 genomic sequence scaffolds and features gene, transcript and CDS annotation tracks. Second, we annotated gene models with gene ontology (GO) terms and InterPro domains which are directly accessible in the browser with links to their entries in the GO (http://www.geneontology.org/) and InterPro (http://www.ebi.ac.uk/interpro/) databases, and we provide transcript and peptide links for sequence downloads. Third, we introduce the transcriptomics of a comprehensive set of developmental stages of O. dioica at high resolution and provide downloadable gene expression data for all developmental stages. Fourth, we incorporate a BLAST tool to identify homologs of genes and proteins. Finally, we include a tutorial that describes how to use OikoBase as well as a link to detailed methods, explaining the data generation and analysis pipeline. OikoBase will provide a valuable resource for research in chordate development, genome evolution and plasticity and the molecular ecology of this important marine planktonic organism.
authors.affiliation: Computational Biology Unit, University of Bergen, Bergen, N-5008, Norway.
authors.forename: Gemma
authors.initials: G
authors.lastname: Danks
authors.forename: Coen
authors.initials: C
authors.lastname: Campsteijn
authors.forename: Mrutyunjaya
authors.initials: M
authors.lastname: Parida
authors.forename: Stephen
authors.initials: S
authors.lastname: Butcher
authors.forename: Harsha
authors.initials: H
authors.lastname: Doddapaneni
authors.forename: Bolei
authors.initials: B
authors.lastname: Fu
authors.forename: Raul
authors.initials: R
authors.lastname: Petrin
authors.forename: Raghu
authors.initials: R
authors.lastname: Metpally
authors.forename: Boris
authors.initials: B
authors.lastname: Lenhard
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.forename: Daniel
authors.initials: D
authors.lastname: Chourrout
authors.forename: Eric M
authors.initials: EM
authors.lastname: Thompson
authors.forename: J Robert
authors.initials: JR
authors.lastname: Manak
mesh_terms: D000818:Animals; D057225:Data Mining; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D023281:Genomics; D020407:Internet; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D059467:Transcriptome; D014561:Urochordata / Q000196:embryology / Q000235:genetics* / Q000254:growth & development