Gramene database in 2010: updates and extensions

被引：109

作者：

Youens-Clark, Ken ^{[1
]}

Buckler, Ed ^{[2
,3
]}

Casstevens, Terry ^{[2
]}

Chen, Charles ^{[4
]}

DeClerck, Genevieve ^{[4
]}

Derwent, Paul ^{[5
]}

Dharmawardhana, Palitha ^{[6
]}

Jaiswal, Pankaj ^{[6
]}

Kersey, Paul ^{[5
]}

Karthikeyan, A. S. ^{[4
]}

Lu, Jerry ^{[1
]}

McCouch, Susan R. ^{[4
]}

Ren, Liya ^{[1
]}

Spooner, William ^{[1
]}

Stein, Joshua C. ^{[1
]}

Thomason, Jim ^{[1
]}

Wei, Sharon ^{[1
]}

Ware, Doreen ^{[1
,3
]}

机构：

[1] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA

[2] Cornell Univ, Inst Genom Divers, Ithaca, NY 14853 USA

[3] Cornell Univ, USDA ARS, NAA Plant Soil & Nutr Lab, Res Unit, Ithaca, NY 14853 USA

[4] Cornell Univ, Dept Genet & Plant Breeding, Ithaca, NY 14853 USA

[5] EMBL European Bioinformat Inst, Cambridge CB10 1SD, England

[6] Oregon State Univ, Dept Bot & Plant Pathol, Corvallis, OR 97331 USA

来源：

NUCLEIC ACIDS RESEARCH | 2011年 / 39卷

基金：

美国国家科学基金会;

关键词：

INFORMATION RESOURCE; PATHWAY DATABASE; GENOME; DUPLICATION; DIVERSITY; ENSEMBL; MOUSE; TOOL;

D O I：

10.1093/nar/gkq1148

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene began with the addition of an Ensembl genome browser and has expanded in the last decade to become a robust resource for plant genomics hosting a wide array of data sets including quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps from various published studies (genetic, physical, bin, etc.). In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data.

引用

页码：D1085 / D1094

页数：10

共 38 条

[1] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[2] A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly [J].

Blankenberg, Daniel ;

Taylor, James ;

Schenck, Ian ;

He, Jianbin ;

Zhang, Yi ;

Ghent, Matthew ;

Veeraraghavan, Narayanan ;

Albert, Istvan ;

Miller, Webb ;

Makova, Kateryna D. ;

Hardison, Ross C. ;

Nekrutenko, Anton .

GENOME RESEARCH, 2007, 17 (06) :960-964

[3] TASSEL: software for association mapping of complex traits in diverse samples [J].

Bradbury, Peter J. ;

Zhang, Zhiwu ;

Kroon, Dallas E. ;

Casstevens, Terry M. ;

Ramdoss, Yogesh ;

Buckler, Edward S. .

BIOINFORMATICS, 2007, 23 (19) :2633-2635

[4] The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases [J].

Caspi, Ron ;

Altman, Tomer ;

Dale, Joseph M. ;

Dreher, Kate ;

Fulcher, Carol A. ;

Gilham, Fred ;

Kaipa, Pallavi ;

Karthikeyan, Athikkattuvalasu S. ;

Kothari, Anamika ;

Krummenacker, Markus ;

Latendresse, Mario ;

Mueller, Lukas A. ;

Paley, Suzanne ;

Popescu, Liviu ;

Pujar, Anuradha ;

Shearer, Alexander G. ;

Zhang, Peifen ;

Karp, Peter D. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D473-D479

[5] Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana [J].

Clark, Richard M. ;

Schweikert, Gabriele ;

Toomajian, Christopher ;

Ossowski, Stephan ;

Zeller, Georg ;

Shinn, Paul ;

Warthmann, Norman ;

Hu, Tina T. ;

Fu, Glenn ;

Hinds, David A. ;

Chen, Huaming ;

Frazer, Kelly A. ;

Huson, Daniel H. ;

Schoelkopf, Bernhard ;

Nordborg, Magnus ;

Raetsch, Gunnar ;

Ecker, Joseph R. ;

Weigel, Detlef .

SCIENCE, 2007, 317 (5836) :338-342

[6] The BioPAX community standard for pathway data sharing [J].

Demir, Emek ;

Cary, Michael P. ;

Paley, Suzanne ;

Fukuda, Ken ;

Lemer, Christian ;

Vastrik, Imre ;

Wu, Guanming ;

D'Eustachio, Peter ;

Schaefer, Carl ;

Luciano, Joanne ;

Schacherer, Frank ;

Martinez-Flores, Irma ;

Hu, Zhenjun ;

Jimenez-Jacinto, Veronica ;

Joshi-Tope, Geeta ;

Kandasamy, Kumaran ;

Lopez-Fuentes, Alejandra C. ;

Mi, Huaiyu ;

Pichler, Elgar ;

Rodchenkov, Igor ;

Splendiani, Andrea ;

Tkachev, Sasha ;

Zucker, Jeremy ;

Gopinath, Gopal ;

Rajasimha, Harsha ;

Ramakrishnan, Ranjani ;

Shah, Imran ;

Syed, Mustafa ;

Anwar, Nadia ;

Babur, Oezguen ;

Blinov, Michael ;

Brauner, Erik ;

Corwin, Dan ;

Donaldson, Sylva ;

Gibbons, Frank ;

Goldberg, Robert ;

Hornbeck, Peter ;

Luna, Augustin ;

Murray-Rust, Peter ;

Neumann, Eric ;

Reubenacker, Oliver ;

Samwald, Matthias ;

van Iersel, Martijn ;

Wimalaratne, Sarala ;

Allen, Keith ;

Braun, Burk ;

Whirl-Carrillo, Michelle ;

Cheung, Kei-Hoi ;

Dahlquist, Kam ;

Finney, Andrew .

NATURE BIOTECHNOLOGY, 2010, 28 (09) :935-942

[7] Ensembl's 10th year [J].

Flicek, Paul ;

Aken, Bronwen L. ;

Ballester, Benoit ;

Beal, Kathryn ;

Bragin, Eugene ;

Brent, Simon ;

Chen, Yuan ;

Clapham, Peter ;

Coates, Guy ;

Fairley, Susan ;

Fitzgerald, Stephen ;

Fernandez-Banet, Julio ;

Gordon, Leo ;

Graef, Stefan ;

Haider, Syed ;

Hammond, Martin ;

Howe, Kerstin ;

Jenkinson, Andrew ;

Johnson, Nathan ;

Kaehaeri, Andreas ;

Keefe, Damian ;

Keenan, Stephen ;

Kinsella, Rhoda ;

Kokocinski, Felix ;

Koscielny, Gautier ;

Kulesha, Eugene ;

Lawson, Daniel ;

Longden, Ian ;

Massingham, Tim ;

McLaren, William ;

Megy, Karine ;

Overduin, Bert ;

Pritchard, Bethan ;

Rios, Daniel ;

Ruffier, Magali ;

Schuster, Michael ;

Slater, Guy ;

Smedley, Damian ;

Spudich, Giulietta ;

Tang, Y. Amy ;

Trevanion, Stephen ;

Vilella, Albert ;

Vogel, Jan ;

White, Simon ;

Wilder, Steven P. ;

Zadissa, Amonida ;

Birney, Ewan ;

Cunningham, Fiona ;

Dunham, Ian ;

Durbin, Richard .

NUCLEIC ACIDS RESEARCH, 2010, 38 :D557-D562

[8] A model diagram layout extension for SBML [J].

Gauges, Ralph ;

Rost, Ursula ;

Sahle, Sven ;

Wegner, Katja .

BIOINFORMATICS, 2006, 22 (15) :1879-1885

[9] DAGchainer: a tool for mining segmental genome duplications and synteny [J].

Haas, BJ ;

Delcher, AL ;

Wortman, JR ;

Salzberg, SL .

BIOINFORMATICS, 2004, 20 (18) :3643-3646

[10] The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla [J].

Jaillon, Olivier ;

Aury, Jean-Marc ;

Noel, Benjamin ;

Policriti, Alberto ;

Clepet, Christian ;

Casagrande, Alberto ;

Choisne, Nathalie ;

Aubourg, Sebastien ;

Vitulo, Nicola ;

Jubin, Claire ;

Vezzi, Alessandro ;

Legeai, Fabrice ;

Hugueney, Philippe ;

Dasilva, Corinne ;

Horner, David ;

Mica, Erica ;

Jublot, Delphine ;

Poulain, Julie ;

Bruyère, Clemence ;

Billault, Alain ;

Segurens, Beatrice ;

Gouyvenoux, Michel ;

Ugarte, Edgardo ;

Cattonaro, Federica ;

Anthouard, Veronique ;

Vico, Virginie ;

Del Fabbro, Cristian ;

Alaux, Michael ;

Di Gaspero, Gabriele ;

Dumas, Vincent ;

Felice, Nicoletta ;

Paillard, Sophie ;

Juman, Irena ;

Moroldo, Marco ;

Scalabrin, Simone ;

Canaguier, Aurelie ;

Le Clainche, Isabelle ;

Malacrida, Giorgio ;

Durand, Eleonore ;

Pesole, Graziano ;

Laucou, Valerie ;

Chatelet, Philippe ;

Merdinoglu, Didier ;

Delledonne, Massimo ;

Pezzotti, Mario ;

Lecharny, Alain ;

Scarpelli, Claude ;

Artiguenave, Francois ;

Pè, M. Enrico ;

Valle, Giorgio .

NATURE, 2007, 449 (7161) :463-U5

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