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Literature DB >> 15489335

Human ORFeome version 1.1: a platform for reverse proteomics.

Jean-François Rual¹, Tomoko Hirozane-Kishikawa, Tong Hao, Nicolas Bertin, Siming Li, Amélie Dricot, Ning Li, Jennifer Rosenberg, Philippe Lamesch, Pierre-Olivier Vidalain, Tracey R Clingingsmith, James L Hartley, Dominic Esposito, David Cheo, Troy Moore, Blake Simmons, Reynaldo Sequerra, Stephanie Bosak, Lynn Doucette-Stamm, Christian Le Peuch, Jean Vandenhaute, Michael E Cusick, Joanna S Albala, David E Hill, Marc Vidal.

Abstract

The advent of systems biology necessitates the cloning of nearly entire sets of protein-encoding open reading frames (ORFs), or ORFeomes, to allow functional studies of the corresponding proteomes. Here, we describe the generation of a first version of the human ORFeome using a newly improved Gateway recombinational cloning approach. Using the Mammalian Gene Collection (MGC) resource as a starting point, we report the successful cloning of 8076 human ORFs, representing at least 7263 human genes, as mini-pools of PCR-amplified products. These were assembled into the human ORFeome version 1.1 (hORFeome v1.1) collection. After assessing the overall quality of this version, we describe the use of hORFeome v1.1 for heterologous protein expression in two different expression systems at proteome scale. The hORFeome v1.1 represents a central resource for the cloning of large sets of human ORFs in various settings for functional proteomics of many types, and will serve as the foundation for subsequent improved versions of the human ORFeome.

Entities: Gene Species

Mesh：

Substances：
Recombinant Proteins

Year: 2004 PMID： 15489335 PMCID： PMC528929 DOI： 10.1101/gr.2973604

Source DB: PubMed Journal: Genome Res ISSN： 1088-9051 Impact factor: 9.043

39 in total

1. Initial sequencing and analysis of the human genome.

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Journal: Nature Date: 2001-02-15 Impact factor: 49.962

2. DNA cloning using in vitro site-specific recombination.

Authors: J L Hartley; G F Temple; M A Brasch
Journal: Genome Res Date: 2000-11 Impact factor: 9.043

3. GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes.

Authors: A J Walhout; G F Temple; M A Brasch; J L Hartley; M A Lorson; S van den Heuvel; M Vidal
Journal: Methods Enzymol Date: 2000 Impact factor: 1.600

Review 4. A new approach to decoding life: systems biology.

Authors: T Ideker; T Galitski; L Hood
Journal: Annu Rev Genomics Hum Genet Date: 2001 Impact factor: 8.929

5. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.

Authors: Yuen Ho; Albrecht Gruhler; Adrian Heilbut; Gary D Bader; Lynda Moore; Sally-Lin Adams; Anna Millar; Paul Taylor; Keiryn Bennett; Kelly Boutilier; Lingyun Yang; Cheryl Wolting; Ian Donaldson; Søren Schandorff; Juanita Shewnarane; Mai Vo; Joanne Taggart; Marilyn Goudreault; Brenda Muskat; Cris Alfarano; Danielle Dewar; Zhen Lin; Katerina Michalickova; Andrew R Willems; Holly Sassi; Peter A Nielsen; Karina J Rasmussen; Jens R Andersen; Lene E Johansen; Lykke H Hansen; Hans Jespersen; Alexandre Podtelejnikov; Eva Nielsen; Janne Crawford; Vibeke Poulsen; Birgitte D Sørensen; Jesper Matthiesen; Ronald C Hendrickson; Frank Gleeson; Tony Pawson; Michael F Moran; Daniel Durocher; Matthias Mann; Christopher W V Hogue; Daniel Figeys; Mike Tyers
Journal: Nature Date: 2002-01-10 Impact factor: 49.962

6. Global analysis of protein activities using proteome chips.

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Journal: Science Date: 2001-07-26 Impact factor: 47.728

7. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.

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Journal: Nature Date: 2000-12-14 Impact factor: 49.962

8. The sequence of the human genome.

Authors: J C Venter; M D Adams; E W Myers; P W Li; R J Mural; G G Sutton; H O Smith; M Yandell; C A Evans; R A Holt; J D Gocayne; P Amanatides; R M Ballew; D H Huson; J R Wortman; Q Zhang; C D Kodira; X H Zheng; L Chen; M Skupski; G Subramanian; P D Thomas; J Zhang; G L Gabor Miklos; C Nelson; S Broder; A G Clark; J Nadeau; V A McKusick; N Zinder; A J Levine; R J Roberts; M Simon; C Slayman; M Hunkapiller; R Bolanos; A Delcher; I Dew; D Fasulo; M Flanigan; L Florea; A Halpern; S Hannenhalli; S Kravitz; S Levy; C Mobarry; K Reinert; K Remington; J Abu-Threideh; E Beasley; K Biddick; V Bonazzi; R Brandon; M Cargill; I Chandramouliswaran; R Charlab; K Chaturvedi; Z Deng; V Di Francesco; P Dunn; K Eilbeck; C Evangelista; A E Gabrielian; W Gan; W Ge; F Gong; Z Gu; P Guan; T J Heiman; M E Higgins; R R Ji; Z Ke; K A Ketchum; Z Lai; Y Lei; Z Li; J Li; Y Liang; X Lin; F Lu; G V Merkulov; N Milshina; H M Moore; A K Naik; V A Narayan; B Neelam; D Nusskern; D B Rusch; S Salzberg; W Shao; B Shue; J Sun; Z Wang; A Wang; X Wang; J Wang; M Wei; R Wides; C Xiao; C Yan; A Yao; J Ye; M Zhan; W Zhang; H Zhang; Q Zhao; L Zheng; F Zhong; W Zhong; S Zhu; S Zhao; D Gilbert; S Baumhueter; G Spier; C Carter; A Cravchik; T Woodage; F Ali; H An; A Awe; D Baldwin; H Baden; M Barnstead; I Barrow; K Beeson; D Busam; A Carver; A Center; M L Cheng; L Curry; S Danaher; L Davenport; R Desilets; S Dietz; K Dodson; L Doup; S Ferriera; N Garg; A Gluecksmann; B Hart; J Haynes; C Haynes; C Heiner; S Hladun; D Hostin; J Houck; T Howland; C Ibegwam; J Johnson; F Kalush; L Kline; S Koduru; A Love; F Mann; D May; S McCawley; T McIntosh; I McMullen; M Moy; L Moy; B Murphy; K Nelson; C Pfannkoch; E Pratts; V Puri; H Qureshi; M Reardon; R Rodriguez; Y H Rogers; D Romblad; B Ruhfel; R Scott; C Sitter; M Smallwood; E Stewart; R Strong; E Suh; R Thomas; N N Tint; S Tse; C Vech; G Wang; J Wetter; S Williams; M Williams; S Windsor; E Winn-Deen; K Wolfe; J Zaveri; K Zaveri; J F Abril; R Guigó; M J Campbell; K V Sjolander; B Karlak; A Kejariwal; H Mi; B Lazareva; T Hatton; A Narechania; K Diemer; A Muruganujan; N Guo; S Sato; V Bafna; S Istrail; R Lippert; R Schwartz; B Walenz; S Yooseph; D Allen; A Basu; J Baxendale; L Blick; M Caminha; J Carnes-Stine; P Caulk; Y H Chiang; M Coyne; C Dahlke; A Deslattes Mays; M Dombroski; M Donnelly; D Ely; S Esparham; C Fosler; H Gire; S Glanowski; K Glasser; A Glodek; M Gorokhov; K Graham; B Gropman; M Harris; J Heil; S Henderson; J Hoover; D Jennings; C Jordan; J Jordan; J Kasha; L Kagan; C Kraft; A Levitsky; M Lewis; X Liu; J Lopez; D Ma; W Majoros; J McDaniel; S Murphy; M Newman; T Nguyen; N Nguyen; M Nodell; S Pan; J Peck; M Peterson; W Rowe; R Sanders; J Scott; M Simpson; T Smith; A Sprague; T Stockwell; R Turner; E Venter; M Wang; M Wen; D Wu; M Wu; A Xia; A Zandieh; X Zhu
Journal: Science Date: 2001-02-16 Impact factor: 47.728

Review 9. Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm.

Authors: A J Walhout; S J Boulton; M Vidal
Journal: Yeast Date: 2000-06-30 Impact factor: 3.239

10. The genome sequence of Drosophila melanogaster.

Authors: M D Adams; S E Celniker; R A Holt; C A Evans; J D Gocayne; P G Amanatides; S E Scherer; P W Li; R A Hoskins; R F Galle; R A George; S E Lewis; S Richards; M Ashburner; S N Henderson; G G Sutton; J R Wortman; M D Yandell; Q Zhang; L X Chen; R C Brandon; Y H Rogers; R G Blazej; M Champe; B D Pfeiffer; K H Wan; C Doyle; E G Baxter; G Helt; C R Nelson; G L Gabor; J F Abril; A Agbayani; H J An; C Andrews-Pfannkoch; D Baldwin; R M Ballew; A Basu; J Baxendale; L Bayraktaroglu; E M Beasley; K Y Beeson; P V Benos; B P Berman; D Bhandari; S Bolshakov; D Borkova; M R Botchan; J Bouck; P Brokstein; P Brottier; K C Burtis; D A Busam; H Butler; E Cadieu; A Center; I Chandra; J M Cherry; S Cawley; C Dahlke; L B Davenport; P Davies; B de Pablos; A Delcher; Z Deng; A D Mays; I Dew; S M Dietz; K Dodson; L E Doup; M Downes; S Dugan-Rocha; B C Dunkov; P Dunn; K J Durbin; C C Evangelista; C Ferraz; S Ferriera; W Fleischmann; C Fosler; A E Gabrielian; N S Garg; W M Gelbart; K Glasser; A Glodek; F Gong; J H Gorrell; Z Gu; P Guan; M Harris; N L Harris; D Harvey; T J Heiman; J R Hernandez; J Houck; D Hostin; K A Houston; T J Howland; M H Wei; C Ibegwam; M Jalali; F Kalush; G H Karpen; Z Ke; J A Kennison; K A Ketchum; B E Kimmel; C D Kodira; C Kraft; S Kravitz; D Kulp; Z Lai; P Lasko; Y Lei; A A Levitsky; J Li; Z Li; Y Liang; X Lin; X Liu; B Mattei; T C McIntosh; M P McLeod; D McPherson; G Merkulov; N V Milshina; C Mobarry; J Morris; A Moshrefi; S M Mount; M Moy; B Murphy; L Murphy; D M Muzny; D L Nelson; D R Nelson; K A Nelson; K Nixon; D R Nusskern; J M Pacleb; M Palazzolo; G S Pittman; S Pan; J Pollard; V Puri; M G Reese; K Reinert; K Remington; R D Saunders; F Scheeler; H Shen; B C Shue; I Sidén-Kiamos; M Simpson; M P Skupski; T Smith; E Spier; A C Spradling; M Stapleton; R Strong; E Sun; R Svirskas; C Tector; R Turner; E Venter; A H Wang; X Wang; Z Y Wang; D A Wassarman; G M Weinstock; J Weissenbach; S M Williams; K C Worley; D Wu; S Yang; Q A Yao; J Ye; R F Yeh; J S Zaveri; M Zhan; G Zhang; Q Zhao; L Zheng; X H Zheng; F N Zhong; W Zhong; X Zhou; S Zhu; X Zhu; H O Smith; R A Gibbs; E W Myers; G M Rubin; J C Venter
Journal: Science Date: 2000-03-24 Impact factor: 47.728

109 in total

1. Generation and comprehensive analysis of an influenza virus polymerase cellular interaction network.

Authors: Lionel Tafforeau; Thibault Chantier; Fabrine Pradezynski; Johann Pellet; Philippe E Mangeot; Pierre-Olivier Vidalain; Patrice Andre; Chantal Rabourdin-Combe; Vincent Lotteau
Journal: J Virol Date: 2011-10-12 Impact factor: 5.103

2. Overlapping functions of Hdac1 and Hdac2 in cell cycle regulation and haematopoiesis.

Authors: Roel H Wilting; Eva Yanover; Marinus R Heideman; Heinz Jacobs; James Horner; Jaco van der Torre; Ronald A DePinho; Jan-Hermen Dannenberg
Journal: EMBO J Date: 2010-06-22 Impact factor: 11.598

3. Compartmentalized Ras proteins transform NIH 3T3 cells with different efficiencies.

Authors: Chiang-Min Cheng; Huiling Li; Stéphane Gasman; Jian Huang; Rachel Schiff; Eric C Chang
Journal: Mol Cell Biol Date: 2010-12-28 Impact factor: 4.272

Review 4. The New State of the Art: Cas9 for Gene Activation and Repression.

Authors: Marie F La Russa; Lei S Qi
Journal: Mol Cell Biol Date: 2015-09-14 Impact factor: 4.272

5. ARAD proteins associated with pectic Arabinan biosynthesis form complexes when transiently overexpressed in planta.

Authors: Jesper Harholt; Jacob Krüger Jensen; Yves Verhertbruggen; Casper Søgaard; Sophie Bernard; Majse Nafisi; Christian Peter Poulsen; Naomi Geshi; Yumiko Sakuragi; Azeddine Driouich; J Paul Knox; Henrik Vibe Scheller
Journal: Planta Date: 2012-01-21 Impact factor: 4.116

6. The alliance for cellular signaling plasmid collection: a flexible resource for protein localization studies and signaling pathway analysis.

Authors: Joelle R Zavzavadjian; Sam Couture; Wei Sun Park; James Whalen; Stephen Lyon; Genie Lee; Eileen Fung; Qingli Mi; Jamie Liu; Estelle Wall; Leah Santat; Kavitha Dhandapani; Christine Kivork; Adrienne Driver; Xiaocui Zhu; Mi Sook Chang; Baljinder Randhawa; Elizabeth Gehrig; Heather Bryan; Mary Verghese; Andreia Maer; Brian Saunders; Yuhong Ning; Shankar Subramaniam; Tobias Meyer; Melvin I Simon; Nancy O'Rourke; Grischa Chandy; Iain D C Fraser
Journal: Mol Cell Proteomics Date: 2006-12-27 Impact factor: 5.911

7. Enzyme free cloning for high throughput gene cloning and expression.

Authors: Rob N de Jong; Mark A Daniëls; Rob Kaptein; Gert E Folkers
Journal: J Struct Funct Genomics Date: 2007-02-13

8. Engineering and Functional Characterization of Fusion Genes Identifies Novel Oncogenic Drivers of Cancer.

Authors: Hengyu Lu; Nicole Villafane; Turgut Dogruluk; Caitlin L Grzeskowiak; Kathleen Kong; Yiu Huen Tsang; Oksana Zagorodna; Angeliki Pantazi; Lixing Yang; Nicholas J Neill; Young Won Kim; Chad J Creighton; Roel G Verhaak; Gordon B Mills; Peter J Park; Raju Kucherlapati; Kenneth L Scott
Journal: Cancer Res Date: 2017-05-16 Impact factor: 12.701

9. Widespread macromolecular interaction perturbations in human genetic disorders.

Authors: Nidhi Sahni; Song Yi; Mikko Taipale; Juan I Fuxman Bass; Jasmin Coulombe-Huntington; Fan Yang; Jian Peng; Jochen Weile; Georgios I Karras; Yang Wang; István A Kovács; Atanas Kamburov; Irina Krykbaeva; Mandy H Lam; George Tucker; Vikram Khurana; Amitabh Sharma; Yang-Yu Liu; Nozomu Yachie; Quan Zhong; Yun Shen; Alexandre Palagi; Adriana San-Miguel; Changyu Fan; Dawit Balcha; Amelie Dricot; Daniel M Jordan; Jennifer M Walsh; Akash A Shah; Xinping Yang; Ani K Stoyanova; Alex Leighton; Michael A Calderwood; Yves Jacob; Michael E Cusick; Kourosh Salehi-Ashtiani; Luke J Whitesell; Shamil Sunyaev; Bonnie Berger; Albert-László Barabási; Benoit Charloteaux; David E Hill; Tong Hao; Frederick P Roth; Yu Xia; Albertha J M Walhout; Susan Lindquist; Marc Vidal
Journal: Cell Date: 2015-04-23 Impact factor: 41.582

Review 10. High-throughput cloning and expression library creation for functional proteomics.

Authors: Fernanda Festa; Jason Steel; Xiaofang Bian; Joshua Labaer
Journal: Proteomics Date: 2013-04-05 Impact factor: 3.984