Literature DB >> 14681461

The Mouse Genome Database (MGD): integrating biology with the genome.

Carol J Bult1, Judith A Blake, Joel E Richardson, James A Kadin, Janan T Eppig, R M Baldarelli, K Barsanti, M Baya, J S Beal, W J Boddy, D W Bradt, D L Burkart, N E Butler, J Campbell, R Corey, L E Corbani, S Cousins, H Dene, H J Drabkin, K Frazer, D M Garippa, L H Glass, C W Goldsmith, P L Grant, B L King, M Lennon-Pierce, J Lewis, I Lu, C M Lutz, L J Maltais, L M McKenzie, D Miers, D Modrusan, L Ni, J E Ormsby, D Qi, S Ramachandran, T B K Reddy, D J Reed, R Sinclair, D R Shaw, C L Smith, P Szauter, B Taylor, P Vanden Borre, M Walker, L Washburn, I Witham, J Winslow, Y Zhu.   

Abstract

The Mouse Genome Database (MGD) is one component of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a community database resource for the laboratory mouse. MGD strives to provide a comprehensive knowledgebase about the mouse with experiments and data annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genetic, genotype (sequence) and phenotype information including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent developments in MGD discussed here include an extensive integration of the mouse sequence data and substantial revisions in the presentation, query and visualization of sequence data.

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Year:  2004        PMID: 14681461      PMCID: PMC308859          DOI: 10.1093/nar/gkh125

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  9 in total

1.  Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Authors:  Y Okazaki; M Furuno; T Kasukawa; J Adachi; H Bono; S Kondo; I Nikaido; N Osato; R Saito; H Suzuki; I Yamanaka; H Kiyosawa; K Yagi; Y Tomaru; Y Hasegawa; A Nogami; C Schönbach; T Gojobori; R Baldarelli; D P Hill; C Bult; D A Hume; J Quackenbush; L M Schriml; A Kanapin; H Matsuda; S Batalov; K W Beisel; J A Blake; D Bradt; V Brusic; C Chothia; L E Corbani; S Cousins; E Dalla; T A Dragani; C F Fletcher; A Forrest; K S Frazer; T Gaasterland; M Gariboldi; C Gissi; A Godzik; J Gough; S Grimmond; S Gustincich; N Hirokawa; I J Jackson; E D Jarvis; A Kanai; H Kawaji; Y Kawasawa; R M Kedzierski; B L King; A Konagaya; I V Kurochkin; Y Lee; B Lenhard; P A Lyons; D R Maglott; L Maltais; L Marchionni; L McKenzie; H Miki; T Nagashima; K Numata; T Okido; W J Pavan; G Pertea; G Pesole; N Petrovsky; R Pillai; J U Pontius; D Qi; S Ramachandran; T Ravasi; J C Reed; D J Reed; J Reid; B Z Ring; M Ringwald; A Sandelin; C Schneider; C A M Semple; M Setou; K Shimada; R Sultana; Y Takenaka; M S Taylor; R D Teasdale; M Tomita; R Verardo; L Wagner; C Wahlestedt; Y Wang; Y Watanabe; C Wells; L G Wilming; A Wynshaw-Boris; M Yanagisawa; I Yang; L Yang; Z Yuan; M Zavolan; Y Zhu; A Zimmer; P Carninci; N Hayatsu; T Hirozane-Kishikawa; H Konno; M Nakamura; N Sakazume; K Sato; T Shiraki; K Waki; J Kawai; K Aizawa; T Arakawa; S Fukuda; A Hara; W Hashizume; K Imotani; Y Ishii; M Itoh; I Kagawa; A Miyazaki; K Sakai; D Sasaki; K Shibata; A Shinagawa; A Yasunishi; M Yoshino; R Waterston; E S Lander; J Rogers; E Birney; Y Hayashizaki
Journal:  Nature       Date:  2002-12-05       Impact factor: 49.962

2.  Initial sequencing and comparative analysis of the mouse genome.

Authors:  Robert H Waterston; Kerstin Lindblad-Toh; Ewan Birney; Jane Rogers; Josep F Abril; Pankaj Agarwal; Richa Agarwala; Rachel Ainscough; Marina Alexandersson; Peter An; Stylianos E Antonarakis; John Attwood; Robert Baertsch; Jonathon Bailey; Karen Barlow; Stephan Beck; Eric Berry; Bruce Birren; Toby Bloom; Peer Bork; Marc Botcherby; Nicolas Bray; Michael R Brent; Daniel G Brown; Stephen D Brown; Carol Bult; John Burton; Jonathan Butler; Robert D Campbell; Piero Carninci; Simon Cawley; Francesca Chiaromonte; Asif T Chinwalla; Deanna M Church; Michele Clamp; Christopher Clee; Francis S Collins; Lisa L Cook; Richard R Copley; Alan Coulson; Olivier Couronne; James Cuff; Val Curwen; Tim Cutts; Mark Daly; Robert David; Joy Davies; Kimberly D Delehaunty; Justin Deri; Emmanouil T Dermitzakis; Colin Dewey; Nicholas J Dickens; Mark Diekhans; Sheila Dodge; Inna Dubchak; Diane M Dunn; Sean R Eddy; Laura Elnitski; Richard D Emes; Pallavi Eswara; Eduardo Eyras; Adam Felsenfeld; Ginger A Fewell; Paul Flicek; Karen Foley; Wayne N Frankel; Lucinda A Fulton; Robert S Fulton; Terrence S Furey; Diane Gage; Richard A Gibbs; Gustavo Glusman; Sante Gnerre; Nick Goldman; Leo Goodstadt; Darren Grafham; Tina A Graves; Eric D Green; Simon Gregory; Roderic Guigó; Mark Guyer; Ross C Hardison; David Haussler; Yoshihide Hayashizaki; LaDeana W Hillier; Angela Hinrichs; Wratko Hlavina; Timothy Holzer; Fan Hsu; Axin Hua; Tim Hubbard; Adrienne Hunt; Ian Jackson; David B Jaffe; L Steven Johnson; Matthew Jones; Thomas A Jones; Ann Joy; Michael Kamal; Elinor K Karlsson; Donna Karolchik; Arkadiusz Kasprzyk; Jun Kawai; Evan Keibler; Cristyn Kells; W James Kent; Andrew Kirby; Diana L Kolbe; Ian Korf; Raju S Kucherlapati; Edward J Kulbokas; David Kulp; Tom Landers; J P Leger; Steven Leonard; Ivica Letunic; Rosie Levine; Jia Li; Ming Li; Christine Lloyd; Susan Lucas; Bin Ma; Donna R Maglott; Elaine R Mardis; Lucy Matthews; Evan Mauceli; John H Mayer; Megan McCarthy; W Richard McCombie; Stuart McLaren; Kirsten McLay; John D McPherson; Jim Meldrim; Beverley Meredith; Jill P Mesirov; Webb Miller; Tracie L Miner; Emmanuel Mongin; Kate T Montgomery; Michael Morgan; Richard Mott; James C Mullikin; Donna M Muzny; William E Nash; Joanne O Nelson; Michael N Nhan; Robert Nicol; Zemin Ning; Chad Nusbaum; Michael J O'Connor; Yasushi Okazaki; Karen Oliver; Emma Overton-Larty; Lior Pachter; Genís Parra; Kymberlie H Pepin; Jane Peterson; Pavel Pevzner; Robert Plumb; Craig S Pohl; Alex Poliakov; Tracy C Ponce; Chris P Ponting; Simon Potter; Michael Quail; Alexandre Reymond; Bruce A Roe; Krishna M Roskin; Edward M Rubin; Alistair G Rust; Ralph Santos; Victor Sapojnikov; Brian Schultz; Jörg Schultz; Matthias S Schwartz; Scott Schwartz; Carol Scott; Steven Seaman; Steve Searle; Ted Sharpe; Andrew Sheridan; Ratna Shownkeen; Sarah Sims; Jonathan B Singer; Guy Slater; Arian Smit; Douglas R Smith; Brian Spencer; Arne Stabenau; Nicole Stange-Thomann; Charles Sugnet; Mikita Suyama; Glenn Tesler; Johanna Thompson; David Torrents; Evanne Trevaskis; John Tromp; Catherine Ucla; Abel Ureta-Vidal; Jade P Vinson; Andrew C Von Niederhausern; Claire M Wade; Melanie Wall; Ryan J Weber; Robert B Weiss; Michael C Wendl; Anthony P West; Kris Wetterstrand; Raymond Wheeler; Simon Whelan; Jamey Wierzbowski; David Willey; Sophie Williams; Richard K Wilson; Eitan Winter; Kim C Worley; Dudley Wyman; Shan Yang; Shiaw-Pyng Yang; Evgeny M Zdobnov; Michael C Zody; Eric S Lander
Journal:  Nature       Date:  2002-12-05       Impact factor: 49.962

3.  Development and evaluation of an automated annotation pipeline and cDNA annotation system.

Authors:  Takeya Kasukawa; Masaaki Furuno; Itoshi Nikaido; Hidemasa Bono; David A Hume; Carol Bult; David P Hill; Richard Baldarelli; Julian Gough; Alexander Kanapin; Hideo Matsuda; Lynn M Schriml; Yoshihide Hayashizaki; Yasushi Okazaki; John Quackenbush
Journal:  Genome Res       Date:  2003-06       Impact factor: 9.043

4.  The Mouse Genome Database (MGD): the model organism database for the laboratory mouse.

Authors:  Judith A Blake; Joel E Richardson; Carol J Bult; Jim A Kadin; Janan T Eppig
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

5.  The mammalian gene collection.

Authors:  R L Strausberg; E A Feingold; R D Klausner; F S Collins
Journal:  Science       Date:  1999-10-15       Impact factor: 47.728

6.  The mouse Gene Expression Database (GXD): updates and enhancements.

Authors:  David P Hill; Dale A Begley; Jacqueline H Finger; Terry F Hayamizu; Ingeborg J McCright; Constance M Smith; Jon S Beal; Lori E Corbani; Judith A Blake; Janan T Eppig; James A Kadin; Joel E Richardson; Martin Ringwald
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

7.  MGD: the Mouse Genome Database.

Authors:  Judith A Blake; Joel E Richardson; Carol J Bult; Jim A Kadin; Janan T Eppig
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

8.  Connecting sequence and biology in the laboratory mouse.

Authors:  Richard M Baldarelli; David P Hill; Judith A Blake; Jun Adachi; Masaaki Furuno; Dirck Bradt; Lori E Corbani; Sharon Cousins; Kenneth S Frazer; Dong Qi; Longlong Yang; Sridhar Ramachandran; Deborah Reed; Yunxia Zhu; Takeya Kasukawa; Martin Ringwald; Benjamin L King; Lois J Maltais; Louise M McKenzie; Lynn M Schriml; Donna Maglott; Deanna M Church; Kim Pruitt; Janan T Eppig; Joel E Richardson; Jim A Kadin; Carol J Bult
Journal:  Genome Res       Date:  2003-06       Impact factor: 9.043

9.  Integrating computationally assembled mouse transcript sequences with the Mouse Genome Informatics (MGI) database.

Authors:  Yunxia Zhu; Benjamin L King; Babak Parvizi; Brian P Brunk; Christian J Stoeckert; John Quackenbush; Joel Richardson; Carol J Bult
Journal:  Genome Biol       Date:  2003-02-03       Impact factor: 13.583

  9 in total
  33 in total

1.  GOblet: a platform for Gene Ontology annotation of anonymous sequence data.

Authors:  Detlef Groth; Hans Lehrach; Steffen Hennig
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

Review 2.  An overview of Ensembl.

Authors:  Ewan Birney; T Daniel Andrews; Paul Bevan; Mario Caccamo; Yuan Chen; Laura Clarke; Guy Coates; James Cuff; Val Curwen; Tim Cutts; Thomas Down; Eduardo Eyras; Xose M Fernandez-Suarez; Paul Gane; Brian Gibbins; James Gilbert; Martin Hammond; Hans-Rudolf Hotz; Vivek Iyer; Kerstin Jekosch; Andreas Kahari; Arek Kasprzyk; Damian Keefe; Stephen Keenan; Heikki Lehvaslaiho; Graham McVicker; Craig Melsopp; Patrick Meidl; Emmanuel Mongin; Roger Pettett; Simon Potter; Glenn Proctor; Mark Rae; Steve Searle; Guy Slater; Damian Smedley; James Smith; Will Spooner; Arne Stabenau; James Stalker; Roy Storey; Abel Ureta-Vidal; K Cara Woodwark; Graham Cameron; Richard Durbin; Anthony Cox; Tim Hubbard; Michele Clamp
Journal:  Genome Res       Date:  2004-04-12       Impact factor: 9.043

3.  Visualizing information across multidimensional post-genomic structured and textual databases.

Authors:  Ying Tao; Carol Friedman; Yves A Lussier
Journal:  Bioinformatics       Date:  2004-12-14       Impact factor: 6.937

Review 4.  Viral infection and human disease--insights from minimotifs.

Authors:  Krishna Kadaveru; Jay Vyas; Martin R Schiller
Journal:  Front Biosci       Date:  2008-05-01

5.  Variation in homeodomain DNA binding revealed by high-resolution analysis of sequence preferences.

Authors:  Michael F Berger; Gwenael Badis; Andrew R Gehrke; Shaheynoor Talukder; Anthony A Philippakis; Lourdes Peña-Castillo; Trevis M Alleyne; Sanie Mnaimneh; Olga B Botvinnik; Esther T Chan; Faiqua Khalid; Wen Zhang; Daniel Newburger; Savina A Jaeger; Quaid D Morris; Martha L Bulyk; Timothy R Hughes
Journal:  Cell       Date:  2008-06-27       Impact factor: 41.582

Review 6.  The autism diagnosis in translation: shared affect in children and mouse models of ASD.

Authors:  Somer L Bishop; Garet P Lahvis
Journal:  Autism Res       Date:  2011-08-31       Impact factor: 5.216

7.  The mouse Gene Expression Database (GXD): updates and enhancements.

Authors:  David P Hill; Dale A Begley; Jacqueline H Finger; Terry F Hayamizu; Ingeborg J McCright; Constance M Smith; Jon S Beal; Lori E Corbani; Judith A Blake; Janan T Eppig; James A Kadin; Joel E Richardson; Martin Ringwald
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

8.  Tools and strategies for physiological genomics: the Rat Genome Database.

Authors:  Simon N Twigger; Dean Pasko; Jeff Nie; Mary Shimoyama; Susan Bromberg; Dan Campbell; Jiali Chen; Norberto dela Cruz; Chunyu Fan; Cindy Foote; Glenn Harris; Brian Hickmann; Yuan Ji; Weihong Jin; Dawei Li; Jedidiah Mathis; Nataliya Nenasheva; Rajni Nigam; Victoria Petri; Dorothy Reilly; Victor Ruotti; Eric Schauberger; Kathy Seiler; Ronit Slyper; Jennifer Smith; Weiye Wang; Wenhua Wu; Lan Zhao; Angela Zuniga-Meyer; Peter J Tonellato; Anne E Kwitek; Howard J Jacob
Journal:  Physiol Genomics       Date:  2005-08-16       Impact factor: 3.107

9.  Positive selection on MHC class II DRB and DQB genes in the bank vole (Myodes glareolus).

Authors:  Kristin Scherman; Lars Råberg; Helena Westerdahl
Journal:  J Mol Evol       Date:  2014-04-20       Impact factor: 2.395

10.  Looking at cerebellar malformations through text-mined interactomes of mice and humans.

Authors:  Ivan Iossifov; Raul Rodriguez-Esteban; Ilya Mayzus; Kathleen J Millen; Andrey Rzhetsky
Journal:  PLoS Comput Biol       Date:  2009-11-06       Impact factor: 4.475

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