Journal article
OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica
Nucleic acids research, Vol.41(Database issue), pp.D845-D853
01/2013
DOI: 10.1093/nar/gks1159
PMCID: PMC3531137
PMID: 23185044
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.
Details
- Title: Subtitle
- OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica
- Creators
- Gemma Danks - Computational Biology Unit, Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway, Department of Biology, University of Iowa, Department of Biology, Carver Center for Genomics, Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA, Department of Molecular Sciences, Imperial College London and MRC Clinical Sciences Centre, London W12 0NN, UK, Commissariat à l’Énergie Atomique (CEA), Genoscope, 91057 Evry, France and Department of Biology, University of Bergen, Bergen, N-5020, NorwayCoen Campsteijn - Computational Biology Unit, Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway, Department of Biology, University of Iowa, Department of Biology, Carver Center for Genomics, Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA, Department of Molecular Sciences, Imperial College London and MRC Clinical Sciences Centre, London W12 0NN, UK, Commissariat à l’Énergie Atomique (CEA), Genoscope, 91057 Evry, France and Department of Biology, University of Bergen, Bergen, N-5020, NorwayMrutyunjaya Parida - Computational Biology Unit, Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway, Department of Biology, University of Iowa, Department of Biology, Carver Center for Genomics, Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA, Department of Molecular Sciences, Imperial College London and MRC Clinical Sciences Centre, London W12 0NN, UK, Commissariat à l’Énergie Atomique (CEA), Genoscope, 91057 Evry, France and Department of Biology, University of Bergen, Bergen, N-5020, NorwayStephen Butcher - Computational Biology Unit, Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway, Department of Biology, University of Iowa, Department of Biology, Carver Center for Genomics, Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA, Department of Molecular Sciences, Imperial College London and MRC Clinical Sciences Centre, London W12 0NN, UK, Commissariat à l’Énergie Atomique (CEA), Genoscope, 91057 Evry, France and Department of Biology, University of Bergen, Bergen, N-5020, NorwayHarsha Doddapaneni - Computational Biology Unit, Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway, Department of Biology, University of Iowa, Department of Biology, Carver Center for Genomics, Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA, Department of Molecular Sciences, Imperial College London and MRC Clinical Sciences Centre, London W12 0NN, UK, Commissariat à l’Énergie Atomique (CEA), Genoscope, 91057 Evry, France and Department of Biology, University of Bergen, Bergen, N-5020, NorwayBolei Fu - Computational Biology Unit, Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway, Department of Biology, University of Iowa, Department of Biology, Carver Center for Genomics, Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA, Department of Molecular Sciences, Imperial College London and MRC Clinical Sciences Centre, London W12 0NN, UK, Commissariat à l’Énergie Atomique (CEA), Genoscope, 91057 Evry, France and Department of Biology, University of Bergen, Bergen, N-5020, NorwayRaul Petrin - Computational Biology Unit, Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway, Department of Biology, University of Iowa, Department of Biology, Carver Center for Genomics, Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA, Department of Molecular Sciences, Imperial College London and MRC Clinical Sciences Centre, London W12 0NN, UK, Commissariat à l’Énergie Atomique (CEA), Genoscope, 91057 Evry, France and Department of Biology, University of Bergen, Bergen, N-5020, NorwayRaghu Metpally - Computational Biology Unit, Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway, Department of Biology, University of Iowa, Department of Biology, Carver Center for Genomics, Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA, Department of Molecular Sciences, Imperial College London and MRC Clinical Sciences Centre, London W12 0NN, UK, Commissariat à l’Énergie Atomique (CEA), Genoscope, 91057 Evry, France and Department of Biology, University of Bergen, Bergen, N-5020, NorwayBoris Lenhard - Computational Biology Unit, Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway, Department of Biology, University of Iowa, Department of Biology, Carver Center for Genomics, Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA, Department of Molecular Sciences, Imperial College London and MRC Clinical Sciences Centre, London W12 0NN, UK, Commissariat à l’Énergie Atomique (CEA), Genoscope, 91057 Evry, France and Department of Biology, University of Bergen, Bergen, N-5020, NorwayPatrick Wincker - Computational Biology Unit, Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway, Department of Biology, University of Iowa, Department of Biology, Carver Center for Genomics, Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA, Department of Molecular Sciences, Imperial College London and MRC Clinical Sciences Centre, London W12 0NN, UK, Commissariat à l’Énergie Atomique (CEA), Genoscope, 91057 Evry, France and Department of Biology, University of Bergen, Bergen, N-5020, NorwayDaniel Chourrout - Computational Biology Unit, Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway, Department of Biology, University of Iowa, Department of Biology, Carver Center for Genomics, Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA, Department of Molecular Sciences, Imperial College London and MRC Clinical Sciences Centre, London W12 0NN, UK, Commissariat à l’Énergie Atomique (CEA), Genoscope, 91057 Evry, France and Department of Biology, University of Bergen, Bergen, N-5020, NorwayEric M Thompson - Computational Biology Unit, Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway, Department of Biology, University of Iowa, Department of Biology, Carver Center for Genomics, Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA, Department of Molecular Sciences, Imperial College London and MRC Clinical Sciences Centre, London W12 0NN, UK, Commissariat à l’Énergie Atomique (CEA), Genoscope, 91057 Evry, France and Department of Biology, University of Bergen, Bergen, N-5020, NorwayJ. Robert Manak - Computational Biology Unit, Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Department of Biochemistry, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, N-0310, Oslo, Norway, Department of Biology, University of Iowa, Department of Biology, Carver Center for Genomics, Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242 USA, Department of Molecular Sciences, Imperial College London and MRC Clinical Sciences Centre, London W12 0NN, UK, Commissariat à l’Énergie Atomique (CEA), Genoscope, 91057 Evry, France and Department of Biology, University of Bergen, Bergen, N-5020, Norway
- Resource Type
- Journal article
- Publication Details
- Nucleic acids research, Vol.41(Database issue), pp.D845-D853
- DOI
- 10.1093/nar/gks1159
- PMID
- 23185044
- PMCID
- PMC3531137
- NLM abbreviation
- Nucleic Acids Res
- ISSN
- 0305-1048
- eISSN
- 1362-4962
- Publisher
- Oxford University Press
- Language
- English
- Date published
- 01/2013
- Academic Unit
- Stead Family Department of Pediatrics; Biology; Craniofacial Anomalies Research Center; Biochemistry and Molecular Biology
- Record Identifier
- 9984217533902771
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