Contributors
The following OC participants contributed to making the clone collection:
- Dana-Farber Cancer Institute
- DKFZ German Cancer Research Center
- GeneCopoeia, Inc.
- Source BioScience
- Kazusa DNA Research Institute
- DNASU Plasmid Repository at Arizona State University
- PLASMID: DF/HCC DNA Resource Core at Harvard
- Mammalian Gene Collection
- The FANTOM Consortium
- Wellcome Trust Sanger Institute
About OC participants:
Dana-Farber Cancer Institute - Center for Cancer Systems Biology (CCSB)
Selected References:
- Lamesch, P., Li, N, Milstein, S et al. (2006) hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Genomics. 2007 Mar;89(3):307-15. Epub 2007 Jan 5. PMID: 17207965
- Rual JF, Hirozane-Kishikawa T, Hao T, Bertin N, Li S, Dricot A, Li N, Rosenberg J, Lamesch P, Vidalain PO, Clingingsmith TR, Hartley JL, Esposito D, Cheo D, Moore T, Simmons B, Sequerra R, Bosak S, Doucette-Stamm L, Le Peuch C, Vandenhaute J, Cusick ME, Albala JS, Hill DE, Vidal M. Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res 2004;14:2128-2135. PMCID: PMC528929
- Yang X, Boehm JS, Yang X, Salehi-Ashtiani K, Hao T, Shen Y, Lubonja R, Thomas SR, Alkan O, Bhimdi T, Green TM, Johannessen CM, Silver SJ, Nguyen C, Murray RR, Hieronymus H, Balcha D, Fan C, Lin C, Ghamsari L, Vidal M, Hahn WC, Hill DE, Root DE. A public genome-scale lentiviral expression library of human ORFs. Nat Methods 2011;8:659-661. PMCID: PMC3234135
DKFZ German Cancer Research Center
Description: The division Molecular Genome Analysis of the DKFZ has contributed to the ORFeome Collaboration Gateway entry clones covering about 3000 human genes. These clones were generated and analyzed within the German cDNA Consortium. This was initiated in 1996 as the world's second large-scale cDNA analysis project, and aimed at systematically generating, sequencing and annotating full-length cDNAs of human genes [1-4]. Starting from gene identification, the consortium then moved on to the cloning of ORFs encoded in cDNAs to establish and exploit this resource in functional genomics projects. The Division Molecular Genome Analysis (DKFZ) generated the clone resources for sequencing, coordinated the consortium, and carried out warehousing of clones, sequences and annotation. Within the ORFeome Collaboration, the DKFZ has further carried out the annotation of all ORFeome Collaboration clones and sequences, using a bioinformatics pipeline that has been established specifically for this purpose.
Selected References:
- Bechtel S, et al. The full-ORF clone resource of the German cDNA Consortium. BMC Genomics 2007, 8(1):399. PMID: 17974005
- Wiemann, S., Arlt, D., Huber, W., Wellenreuther, R., Schleeger, S., Mehrle, A., Bechtel, S., Sauermann, M., Korf, U., Pepperkok, R., Sultmann, H., Poustka, A. (2004) From ORFeome to Biology: A Functional Genomics Pipeline. Genome Res 14, 2136-44 PMID: 15489336
- Wellenreuther R, Schupp I, Poustka A, Wiemann S, German cDNA Consortium: SMART amplification combined with cDNA size fractionation in order to obtain large full-length clones. BMC Genomics 2004, 5(1):36. PMID: 15198809
- Wiemann S, et al. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. Genome Res 2001, 11(3):422-435. PMID: 11230166
Selected References:
Selected References:
DNASU Plasmid Repository at the Center for Personalized Diagnostics at the Biodesign Institute of Arizona State University
Description: DNASU is a central repository for plasmid clones and collections. Currently we store and distribute over 205,000 plasmids including 75,000 human and mouse plasmids, full genome collections, the protein expression plasmids from the Protein Structure Initiative as the PSI: Biology Material Repository (PSI : Biology-MR), and both small and large collections from individual researchers. We are also a founding member and distributor of the ORFeome Collaboration plasmid collection.
Selected References:
- Seiler CY, Park JG, Sharma A, Hunter P, Surapaneni P, Sedillo C, Field J, Algar R, Price A, Steel J, Throop A, Fiacco M, Labaer J.(2013) DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research. Nucleic Acids Res. 2013 Nov 12. [Epub ahead of print] PMID: 24225319
- Rolfs A, Hu Y, Ebert L, Hoffmann D, Zuo D, Ramachandran N, Raphael J, Kelley F, McCarron S, Jepson DA, Shen B, Baqui MM, Pearlberg J, Taycher E, DeLoughery C, Hoerlein A, Korn B, LaBaer J. (2008) A biomedically enriched collection of 7000 human ORF clones. PLoS One. 2008 Jan 30;3(1):e1528. PMID: 18231609
DNA Resource Core at Harvard Medical School
Selected References:
- Rolfs A, Hu Y, Ebert L, Hoffmann D, Zuo D, Ramachandran N, Raphael J, Kelley F, McCarron S, Jepson DA, Shen B, Baqui MM, Pearlberg J, Taycher E, DeLoughery C, Hoerlein A, Korn B, LaBaer J. (2008) A biomedically enriched collection of 7000 human ORF clones. PLoS One. 2008 Jan 30;3(1):e1528. PMID: 18231609
- Lennon, G.G., Auffray, C., Polymeropoulos, M., Soares, M.B. (1996) The I.M.A.G.E. Consortium: An Integrated Molecular Analysis of Genomes and their Expression. Genomics 33:151-152 PMID: 8617505
Selected References
- Nakajima D, Saito K, Yamakawa H, Kikuno RF, Nakayama M, Ohara R, Okazaki N, Koga H, Nagase T, Ohara O. Preparation of a set of expression-ready clones of mammalian long cDNAs encoding large proteins by the ORF trap cloning method. DNA Res 2005;12:257-267. PMID: 16769688
- Takahiro Nagase, Hisashi Yamakawa, Shinichi Tadokoro, Daisuke Nakajima, Shinichi Inoue, Kei Yamaguchi, Yasuhide Itokawa, Reiko F. Kikuno, Hisashi Koga, and Osamu Ohara (2008). Exploration of Human ORFeome: High-Throughput Preparation of ORF Clones and Efficient Characterization of Their Protein Products. DNA Res. 15: 137 -149 PMID: 18316326
Selected References:
- Strausberg RL et al. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (2002) PNAS99(26):16899-903 PMID: 12477932
- Gerhard DS et al. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (2004) Genome Research 14:2121-7 PMID: 15489334
- Temple G et al. The completion of the Mammalian Gene Collection (MGC). (2009) Genome Research 19:2324-33 PMID: 19767417
Organized by the RIKEN Preventive Medicine & Diagnosis Innovation Program and RIKEN Center for Life Science Technologies - Division of Genomic Technologies
Description: FANTOM is an international research consortium established by Dr. Hayashizaki and his colleagues in 2000 to assign functional annotations to the full-length cDNAs that were collected during the Mouse Encyclopedia Project at RIKEN. FANTOM has since developed and expanded over time to encompass the fields of transcriptome analysis. The object of the project is moving steadily up the layers in the system of life, progressing thus from an understanding of the elements - the transcripts - to an understanding of the system - the transcriptional regulatory network, in other words the system of an individual life form.
Selected References:
- Severin J,et al.(2014) Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. Nat Biotechnol. Mar;32(3):217-9. doi: 10.1038/nbt.2840. PMID: 24727769
- Andersson R, et al; FANTOM Consortium, Forrest AR, Carninci P, Rehli M, Sandelin A.(2014) An atlas of active enhancers across human cell types and tissues. Nature. Mar 27;507(7493):455-61. doi: 10.1038/nature12787. PMID: 24670763
- FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, et al. (2014) A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.PMID: 24670764
- Carninci P, et al FANTOM Consortium; RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group). (2006) The transcriptional landscape of the mammalian genome. Science. 2005 Sep 2;309(5740):1559-63. Erratum in: Science. Mar 24;311(5768):1713. PMID: 16141072
Wellcome Trust Sanger Institute
Selected References:
- Collins JE et al. A genome annotation-driven approach to cloning the human ORFeome. (2004) Genome Biology 5:R84 doi:10.1186/gb-2004-5-10-r84 PMID: 15461802