title: The Xenopus ORFeome: A resource that enables functional genomics.
abstract: Functional characterisation of proteins and large-scale, systems-level studies are enabled by extensive sets of cloned open reading frames (ORFs) in an easily-accessible format that enables many different applications. Here we report the release of the first stage of the Xenopus ORFeome, which contains 8673 ORFs from the Xenopus Gene Collection (XGC) for Xenopus laevis, cloned into a Gateway® donor vector enabling rapid in-frame transfer of the ORFs to expression vectors. This resource represents an estimated 7871 unique genes, approximately 40% of the non-redundant X. laevis gene complement, and includes 2724 genes where the human ortholog has an association with disease. Transfer into the Gateway system was validated by 5' and 3' end sequencing of the entire collection and protein expression of a set of test clones. In a parallel process, the underlying ORF predictions from the original XGC collection were re-analysed to verify quality and full-length status, identifying those proteins likely to exhibit truncations when translated. These data are integrated into Xenbase, the Xenopus community database, which associates genomic, expression, function and human disease model metadata to each ORF, enabling end-users to search for ORFeome clones with links to commercial distributors of the collection. When coupled with the experimental advantages of Xenopus eggs and embryos, the ORFeome collection represents a valuable resource for functional genomics and disease modelling.
authors.affiliation: The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.
authors.forename: Ian M
authors.initials: IM
authors.lastname: Grant
authors.affiliation: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
authors.forename: Dawit
authors.initials: D
authors.lastname: Balcha
authors.affiliation: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
authors.forename: Tong
authors.initials: T
authors.lastname: Hao
authors.affiliation: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
authors.forename: Yun
authors.initials: Y
authors.lastname: Shen
authors.affiliation: University of Virginia, School of Medicine, Charlottesville, VA 22908, USA.
authors.forename: Prasad
authors.initials: P
authors.lastname: Trivedi
authors.affiliation: The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.
authors.forename: Ilya
authors.initials: I
authors.lastname: Patrushev
authors.affiliation: Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
authors.forename: Joshua D
authors.initials: JD
authors.lastname: Fortriede
authors.affiliation: Xenbase, Department of Biological Science, University of Calgary, Calgary, AB, Canada.
authors.forename: John B
authors.initials: JB
authors.lastname: Karpinka
authors.affiliation: University of Virginia, School of Medicine, Charlottesville, VA 22908, USA.
authors.forename: Limin
authors.initials: L
authors.lastname: Liu
authors.affiliation: Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Zorn
authors.affiliation: University of Virginia, School of Medicine, Charlottesville, VA 22908, USA.
authors.forename: P Todd
authors.initials: PT
authors.lastname: Stukenberg
authors.affiliation: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Electronic address: David_Hill@dfci.harvard.edu.
authors.forename: David E
authors.initials: DE
authors.lastname: Hill
authors.affiliation: The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK. Electronic address: mike.gilchrist@crick.ac.uk.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Gilchrist
mesh_terms: D000818:Animals; D001483:Base Sequence; D003001:Cloning, Molecular; D018076:DNA, Complementary / Q000235:genetics; D030541:Databases, Genetic; D004194:Disease / Q000235:genetics; D023281:Genomics; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D014981:Xenopus / Q000235:genetics*; D029867:Xenopus Proteins / Q000235:genetics; D014982:Xenopus laevis / Q000235:genetics
chemical_list: D018076:DNA, Complementary; D029867:Xenopus Proteins
keywords: Gateway; Gene annotation; ORFeome; Open reading frame; Recombinational cloning; Xenopus