Literature DB >> 19767417

The completion of the Mammalian Gene Collection (MGC).

Gary Temple, Daniela S Gerhard, Rebekah Rasooly, Elise A Feingold, Peter J Good, Cristen Robinson, Allison Mandich, Jeffrey G Derge, Jeanne Lewis, Debonny Shoaf, Francis S Collins, Wonhee Jang, Lukas Wagner, Carolyn M Shenmen, Leonie Misquitta, Carl F Schaefer, Kenneth H Buetow, Tom I Bonner, Linda Yankie, Ming Ward, Lon Phan, Alex Astashyn, Garth Brown, Catherine Farrell, Jennifer Hart, Melissa Landrum, Bonnie L Maidak, Michael Murphy, Terence Murphy, Bhanu Rajput, Lillian Riddick, David Webb, Janet Weber, Wendy Wu, Kim D Pruitt, Donna Maglott, Adam Siepel, Brona Brejova, Mark Diekhans, Rachel Harte, Robert Baertsch, Jim Kent, David Haussler, Michael Brent, Laura Langton, Charles L G Comstock, Michael Stevens, Chaochun Wei, Marijke J van Baren, Kourosh Salehi-Ashtiani, Ryan R Murray, Lila Ghamsari, Elizabeth Mello, Chenwei Lin, Christa Pennacchio, Kirsten Schreiber, Nicole Shapiro, Amber Marsh, Elizabeth Pardes, Troy Moore, Anita Lebeau, Mike Muratet, Blake Simmons, David Kloske, Stephanie Sieja, James Hudson, Praveen Sethupathy, Michael Brownstein, Narayan Bhat, Joseph Lazar, Howard Jacob, Chris E Gruber, Mark R Smith, John McPherson, Angela M Garcia, Preethi H Gunaratne, Jiaqian Wu, Donna Muzny, Richard A Gibbs, Alice C Young, Gerard G Bouffard, Robert W Blakesley, Jim Mullikin, Eric D Green, Mark C Dickson, Alex C Rodriguez, Jane Grimwood, Jeremy Schmutz, Richard M Myers, Martin Hirst, Thomas Zeng, Kane Tse, Michelle Moksa, Merinda Deng, Kevin Ma, Diana Mah, Johnson Pang, Greg Taylor, Eric Chuah, Athena Deng, Keith Fichter, Anne Go, Stephanie Lee, Jing Wang, Malachi Griffith, Ryan Morin, Richard A Moore, Michael Mayo, Sarah Munro, Susan Wagner, Steven J M Jones, Robert A Holt, Marco A Marra, Sun Lu, Shuwei Yang, James Hartigan, Marcus Graf, Ralf Wagner, Stanley Letovksy, Jacqueline C Pulido, Keith Robison, Dominic Esposito, James Hartley, Vanessa E Wall, Ralph F Hopkins, Osamu Ohara, Stefan Wiemann.   

Abstract

Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-protein-coding sequence cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random expressed sequence tag screening of cDNA libraries. Here, we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97% of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide.

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Year:  2009        PMID: 19767417      PMCID: PMC2792178          DOI: 10.1101/gr.095976.109

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


  35 in total

1.  Using multiple alignments to improve gene prediction.

Authors:  Samuel S Gross; Michael R Brent
Journal:  J Comput Biol       Date:  2006-03       Impact factor: 1.479

2.  Improving gene annotation using peptide mass spectrometry.

Authors:  Stephen Tanner; Zhouxin Shen; Julio Ng; Liliana Florea; Roderic Guigó; Steven P Briggs; Vineet Bafna
Journal:  Genome Res       Date:  2006-12-22       Impact factor: 9.043

Review 3.  Genome-wide transcription and the implications for genomic organization.

Authors:  Philipp Kapranov; Aarron T Willingham; Thomas R Gingeras
Journal:  Nat Rev Genet       Date:  2007-05-08       Impact factor: 53.242

4.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:  Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal:  Nature       Date:  2007-06-14       Impact factor: 49.962

5.  Targeted discovery of novel human exons by comparative genomics.

Authors:  Adam Siepel; Mark Diekhans; Brona Brejová; Laura Langton; Michael Stevens; Charles L G Comstock; Colleen Davis; Brent Ewing; Shelly Oommen; Christopher Lau; Hung-Chun Yu; Jianfeng Li; Bruce A Roe; Phil Green; Daniela S Gerhard; Gary Temple; David Haussler; Michael R Brent
Journal:  Genome Res       Date:  2007-11-07       Impact factor: 9.043

Review 6.  Raising the estimate of functional human sequences.

Authors:  Michael Pheasant; John S Mattick
Journal:  Genome Res       Date:  2007-08-09       Impact factor: 9.043

7.  The transcriptional landscape of the mammalian genome.

Authors:  P Carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; V B Bajic; S E Brenner; S Batalov; A R R Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; T L Bailey; M Bansal; L Baxter; K W Beisel; T Bersano; H Bono; A M Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; M Gariboldi; P Georgii-Hemming; T R Gingeras; T Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; K Ikeo; A Iwama; T Ishikawa; M Jakt; A Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; G Kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; L Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; L Marchionni; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Y Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; N Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; S L Salzberg; A Sandelin; C Schneider; C Schönbach; K Sekiguchi; C A M Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; E Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; M S Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; W Hide; C Bult; S M Grimmond; R D Teasdale; E T Liu; V Brusic; J Quackenbush; C Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; M Itoh; T Kato; H Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; K Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
Journal:  Science       Date:  2005-09-02       Impact factor: 47.728

8.  Using ESTs to improve the accuracy of de novo gene prediction.

Authors:  Chaochun Wei; Michael R Brent
Journal:  BMC Bioinformatics       Date:  2006-07-03       Impact factor: 3.169

9.  The UCSC Genome Browser Database: 2008 update.

Authors:  D Karolchik; R M Kuhn; R Baertsch; G P Barber; H Clawson; M Diekhans; B Giardine; R A Harte; A S Hinrichs; F Hsu; K M Kober; W Miller; J S Pedersen; A Pohl; B J Raney; B Rhead; K R Rosenbloom; K E Smith; M Stanke; A Thakkapallayil; H Trumbower; T Wang; A S Zweig; D Haussler; W J Kent
Journal:  Nucleic Acids Res       Date:  2007-12-17       Impact factor: 16.971

10.  The vertebrate genome annotation (Vega) database.

Authors:  L G Wilming; J G R Gilbert; K Howe; S Trevanion; T Hubbard; J L Harrow
Journal:  Nucleic Acids Res       Date:  2007-11-14       Impact factor: 16.971

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  70 in total

Review 1.  Life on a microarray: assessing live cell functions in a microarray format.

Authors:  Krisztián Papp; Zoltán Szittner; József Prechl
Journal:  Cell Mol Life Sci       Date:  2012-03-04       Impact factor: 9.261

2.  Advancing RNA-Seq analysis.

Authors:  Brian J Haas; Michael C Zody
Journal:  Nat Biotechnol       Date:  2010-05       Impact factor: 54.908

3.  Towards a map of cis-regulatory sequences in the human genome.

Authors:  Meng Niu; Ehsan Tabari; Pengyu Ni; Zhengchang Su
Journal:  Nucleic Acids Res       Date:  2018-06-20       Impact factor: 16.971

4.  Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing.

Authors:  Jia Qian Wu; Lukas Habegger; Parinya Noisa; Anna Szekely; Caihong Qiu; Stephen Hutchison; Debasish Raha; Michael Egholm; Haifan Lin; Sherman Weissman; Wei Cui; Mark Gerstein; Michael Snyder
Journal:  Proc Natl Acad Sci U S A       Date:  2010-03-01       Impact factor: 11.205

5.  Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity.

Authors:  Aashiq H Kachroo; Jon M Laurent; Christopher M Yellman; Austin G Meyer; Claus O Wilke; Edward M Marcotte
Journal:  Science       Date:  2015-05-22       Impact factor: 47.728

6.  Steroid hormone modulation of RET through two estrogen responsive enhancers in breast cancer.

Authors:  Zachary E Stine; David M McGaughey; Seneca L Bessling; Shengchao Li; Andrew S McCallion
Journal:  Hum Mol Genet       Date:  2011-07-07       Impact factor: 6.150

Review 7.  Between a chicken and a grape: estimating the number of human genes.

Authors:  Mihaela Pertea; Steven L Salzberg
Journal:  Genome Biol       Date:  2010-05-05       Impact factor: 13.583

8.  Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation.

Authors:  Justin King; Justin Foster; James M Davison; John F Rawls; Ghislain Breton
Journal:  Zebrafish       Date:  2017-11-27       Impact factor: 1.985

9.  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

10.  Computational prediction and experimental verification of new MAP kinase docking sites and substrates including Gli transcription factors.

Authors:  Thomas C Whisenant; David T Ho; Ryan W Benz; Jeffrey S Rogers; Robyn M Kaake; Elizabeth A Gordon; Lan Huang; Pierre Baldi; Lee Bardwell
Journal:  PLoS Comput Biol       Date:  2010-08-26       Impact factor: 4.475

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