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Literature DB >> 11752263

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome.

Heiko Schoof¹, Paolo Zaccaria, Heidrun Gundlach, Kai Lemcke, Stephen Rudd, Grigory Kolesov, Roland Arnold, H W Mewes, Klaus F X Mayer.

Abstract

Arabidopsis thaliana is the first plant for which the complete genome has been sequenced and published. Annotation of complex eukaryotic genomes requires more than the assignment of genetic elements to the sequence. Besides completing the list of genes, we need to discover their cellular roles, their regulation and their interactions in order to understand the workings of the whole plant. The MIPS Arabidopsis thaliana Database (MAtDB; http://mips.gsf.de/proj/thal/db) started out as a repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project and the Arabidopsis Genome Initiative. Our aim is to transform MAtDB into an integrated biological knowledge resource by integrating diverse data, tools, query and visualization capabilities and by creating a comprehensive resource for Arabidopsis as a reference model for other species, including crop plants.

Entities: Species

Mesh：

Substances：
Plant Proteins

Year: 2002 PMID： 11752263 PMCID： PMC99069 DOI： 10.1093/nar/30.1.91

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

9 in total

1. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors: M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal: Nat Genet Date: 2000-05 Impact factor: 38.330

2. Functional and structural genomics using PEDANT.

Authors: D Frishman; K Albermann; J Hani; K Heumann; A Metanomski; A Zollner; H W Mewes
Journal: Bioinformatics Date: 2001-01 Impact factor: 6.937

3. MIPS: a database for genomes and protein sequences.

Authors: H W Mewes; D Frishman; C Gruber; B Geier; D Haase; A Kaps; K Lemcke; G Mannhaupt; F Pfeiffer; C Schüller; S Stocker; B Weil
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

4. Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana.

Authors: K Mayer; G Murphy; R Tarchini; R Wambutt; G Volckaert; T Pohl; A Düsterhöft; W Stiekema; K D Entian; N Terryn; K Lemcke; D Haase; C R Hall; A M van Dodeweerd; S V Tingey; H W Mewes; M W Bevan; I Bancroft
Journal: Genome Res Date: 2001-07 Impact factor: 9.043

5. Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.

Authors: K Mayer; C Schüller; R Wambutt; G Murphy; G Volckaert; T Pohl; A Düsterhöft; W Stiekema; K D Entian; N Terryn; B Harris; W Ansorge; P Brandt; L Grivell; M Rieger; M Weichselgartner; V de Simone; B Obermaier; R Mache; M Müller; M Kreis; M Delseny; P Puigdomenech; M Watson; T Schmidtheini; B Reichert; D Portatelle; M Perez-Alonso; M Boutry; I Bancroft; P Vos; J Hoheisel; W Zimmermann; H Wedler; P Ridley; S A Langham; B McCullagh; L Bilham; J Robben; J Van der Schueren; B Grymonprez; Y J Chuang; F Vandenbussche; M Braeken; I Weltjens; M Voet; I Bastiaens; R Aert; E Defoor; T Weitzenegger; G Bothe; U Ramsperger; H Hilbert; M Braun; E Holzer; A Brandt; S Peters; M van Staveren; W Dirske; P Mooijman; R Klein Lankhorst; M Rose; J Hauf; P Kötter; S Berneiser; S Hempel; M Feldpausch; S Lamberth; H Van den Daele; A De Keyser; C Buysshaert; J Gielen; R Villarroel; R De Clercq; M Van Montagu; J Rogers; A Cronin; M Quail; S Bray-Allen; L Clark; J Doggett; S Hall; M Kay; N Lennard; K McLay; R Mayes; A Pettett; M A Rajandream; M Lyne; V Benes; S Rechmann; D Borkova; H Blöcker; M Scharfe; M Grimm; T H Löhnert; S Dose; M de Haan; A Maarse; M Schäfer; S Müller-Auer; C Gabel; M Fuchs; B Fartmann; K Granderath; D Dauner; A Herzl; S Neumann; A Argiriou; D Vitale; R Liguori; E Piravandi; O Massenet; F Quigley; G Clabauld; A Mündlein; R Felber; S Schnabl; R Hiller; W Schmidt; A Lecharny; S Aubourg; F Chefdor; R Cooke; C Berger; A Montfort; E Casacuberta; T Gibbons; N Weber; M Vandenbol; M Bargues; J Terol; A Torres; A Perez-Perez; B Purnelle; E Bent; S Johnson; D Tacon; T Jesse; L Heijnen; S Schwarz; P Scholler; S Heber; P Francs; C Bielke; D Frishman; D Haase; K Lemcke; H W Mewes; S Stocker; P Zaccaria; M Bevan; R K Wilson; M de la Bastide; K Habermann; L Parnell; N Dedhia; L Gnoj; K Schutz; E Huang; L Spiegel; M Sehkon; J Murray; P Sheet; M Cordes; J Abu-Threideh; T Stoneking; J Kalicki; T Graves; G Harmon; J Edwards; P Latreille; L Courtney; J Cloud; A Abbott; K Scott; D Johnson; P Minx; D Bentley; B Fulton; N Miller; T Greco; K Kemp; J Kramer; L Fulton; E Mardis; M Dante; K Pepin; L Hillier; J Nelson; J Spieth; E Ryan; S Andrews; C Geisel; D Layman; H Du; J Ali; A Berghoff; K Jones; K Drone; M Cotton; C Joshu; B Antonoiu; M Zidanic; C Strong; H Sun; B Lamar; C Yordan; P Ma; J Zhong; R Preston; D Vil; M Shekher; A Matero; R Shah; I K Swaby; A O'Shaughnessy; M Rodriguez; J Hoffmann; S Till; S Granat; N Shohdy; A Hasegawa; A Hameed; M Lodhi; A Johnson; E Chen; M Marra; R Martienssen; W R McCombie
Journal: Nature Date: 1999-12-16 Impact factor: 49.962

6. Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny.

Authors: H M Ku; T Vision; J Liu; S D Tanksley
Journal: Proc Natl Acad Sci U S A Date: 2000-08-01 Impact factor: 11.205

7. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.

Authors: S Tabata; T Kaneko; Y Nakamura; H Kotani; T Kato; E Asamizu; N Miyajima; S Sasamoto; T Kimura; T Hosouchi; K Kawashima; M Kohara; M Matsumoto; A Matsuno; A Muraki; S Nakayama; N Nakazaki; K Naruo; S Okumura; S Shinpo; C Takeuchi; T Wada; A Watanabe; M Yamada; M Yasuda; S Sato; M de la Bastide; E Huang; L Spiegel; L Gnoj; A O'Shaughnessy; R Preston; K Habermann; J Murray; D Johnson; T Rohlfing; J Nelson; T Stoneking; K Pepin; J Spieth; M Sekhon; J Armstrong; M Becker; E Belter; H Cordum; M Cordes; L Courtney; W Courtney; M Dante; H Du; J Edwards; J Fryman; B Haakensen; E Lamar; P Latreille; S Leonard; R Meyer; E Mulvaney; P Ozersky; A Riley; C Strowmatt; C Wagner-McPherson; A Wollam; M Yoakum; M Bell; N Dedhia; L Parnell; R Shah; M Rodriguez; L H See; D Vil; J Baker; K Kirchoff; K Toth; L King; A Bahret; B Miller; M Marra; R Martienssen; W R McCombie; R K Wilson; G Murphy; I Bancroft; G Volckaert; R Wambutt; A Düsterhöft; W Stiekema; T Pohl; K D Entian; N Terryn; N Hartley; E Bent; S Johnson; S A Langham; B McCullagh; J Robben; B Grymonprez; W Zimmermann; U Ramsperger; H Wedler; K Balke; E Wedler; S Peters; M van Staveren; W Dirkse; P Mooijman; R K Lankhorst; T Weitzenegger; G Bothe; M Rose; J Hauf; S Berneiser; S Hempel; M Feldpausch; S Lamberth; R Villarroel; J Gielen; W Ardiles; O Bents; K Lemcke; G Kolesov; K Mayer; S Rudd; H Schoof; C Schueller; P Zaccaria; H W Mewes; M Bevan; P Fransz
Journal: Nature Date: 2000-12-14 Impact factor: 49.962

8. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.

Authors: M Salanoubat; K Lemcke; M Rieger; W Ansorge; M Unseld; B Fartmann; G Valle; H Blöcker; M Perez-Alonso; B Obermaier; M Delseny; M Boutry; L A Grivell; R Mache; P Puigdomènech; V De Simone; N Choisne; F Artiguenave; C Robert; P Brottier; P Wincker; L Cattolico; J Weissenbach; W Saurin; F Quétier; M Schäfer; S Müller-Auer; C Gabel; M Fuchs; V Benes; E Wurmbach; H Drzonek; H Erfle; N Jordan; S Bangert; R Wiedelmann; H Kranz; H Voss; R Holland; P Brandt; G Nyakatura; A Vezzi; M D'Angelo; A Pallavicini; S Toppo; B Simionati; A Conrad; K Hornischer; G Kauer; T H Löhnert; G Nordsiek; J Reichelt; M Scharfe; O Schön; M Bargues; J Terol; J Climent; P Navarro; C Collado; A Perez-Perez; B Ottenwälder; D Duchemin; R Cooke; M Laudie; C Berger-Llauro; B Purnelle; D Masuy; M de Haan; A C Maarse; J P Alcaraz; A Cottet; E Casacuberta; A Monfort; A Argiriou; M flores; R Liguori; D Vitale; G Mannhaupt; D Haase; H Schoof; S Rudd; P Zaccaria; H W Mewes; K F Mayer; S Kaul; C D Town; H L Koo; L J Tallon; J Jenkins; T Rooney; M Rizzo; A Walts; T Utterback; C Y Fujii; T P Shea; T H Creasy; B Haas; R Maiti; D Wu; J Peterson; S Van Aken; G Pai; J Militscher; P Sellers; J E Gill; T V Feldblyum; D Preuss; X Lin; W C Nierman; S L Salzberg; O White; J C Venter; C M Fraser; T Kaneko; Y Nakamura; S Sato; T Kato; E Asamizu; S Sasamoto; T Kimura; K Idesawa; K Kawashima; Y Kishida; C Kiyokawa; M Kohara; M Matsumoto; A Matsuno; A Muraki; S Nakayama; N Nakazaki; S Shinpo; C Takeuchi; T Wada; A Watanabe; M Yamada; M Yasuda; S Tabata
Journal: Nature Date: 2000-12-14 Impact factor: 49.962

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

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

9 in total

70 in total

1. Substoichiometric shifting in the plant mitochondrial genome is influenced by a gene homologous to MutS.

Authors: Ricardo V Abdelnoor; Ryan Yule; Annakaisa Elo; Alan C Christensen; Gilbert Meyer-Gauen; Sally A Mackenzie
Journal: Proc Natl Acad Sci U S A Date: 2003-05-01 Impact factor: 11.205

2. An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics.

Authors: Mario G Rosso; Yong Li; Nicolai Strizhov; Bernd Reiss; Koen Dekker; Bernd Weisshaar
Journal: Plant Mol Biol Date: 2003-09 Impact factor: 4.076

3. The carboxylesterase gene family from Arabidopsis thaliana.

Authors: Sean D G Marshall; Joanna J Putterill; Kim M Plummer; Richard D Newcomb
Journal: J Mol Evol Date: 2003-11 Impact factor: 2.395

4. PlantProm: a database of plant promoter sequences.

Authors: Ilham A Shahmuradov; Alex J Gammerman; John M Hancock; Peter M Bramley; Victor V Solovyev
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

5. Sputnik: a database platform for comparative plant genomics.

Authors: Stephen Rudd; Hans-Werner Mewes; Klaus F X Mayer
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

6. Annotation of the Arabidopsis genome.

Authors: Jennifer R Wortman; Brian J Haas; Linda I Hannick; Roger K Smith; Rama Maiti; Catherine M Ronning; Agnes P Chan; Chunhui Yu; Mulu Ayele; Catherine A Whitelaw; Owen R White; Christopher D Town
Journal: Plant Physiol Date: 2003-06 Impact factor: 8.340

7. Nuclear genes that encode mitochondrial proteins for DNA and RNA metabolism are clustered in the Arabidopsis genome.

Authors: Annakaisa Elo; Anna Lyznik; Delkin O Gonzalez; Stephen D Kachman; Sally A Mackenzie
Journal: Plant Cell Date: 2003-07 Impact factor: 11.277

8. Transcriptomic and proteomic analyses of pericycle cells of the maize primary root.

Authors: Diana Dembinsky; Katrin Woll; Muhammad Saleem; Yan Liu; Yan Fu; Lisa A Borsuk; Tobias Lamkemeyer; Claudia Fladerer; Johannes Madlung; Brad Barbazuk; Alfred Nordheim; Dan Nettleton; Patrick S Schnable; Frank Hochholdinger
Journal: Plant Physiol Date: 2007-08-31 Impact factor: 8.340

9. Proteomic survey of metabolic pathways in rice.

Authors: Antonius Koller; Michael P Washburn; B Markus Lange; Nancy L Andon; Cosmin Deciu; Paul A Haynes; Lara Hays; David Schieltz; Ryan Ulaszek; Jing Wei; Dirk Wolters; John R Yates
Journal: Proc Natl Acad Sci U S A Date: 2002-08-05 Impact factor: 11.205

10. MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics.

Authors: Heiko Schoof; Rebecca Ernst; Vladimir Nazarov; Lukas Pfeifer; Hans-Werner Mewes; Klaus F X Mayer
Journal: Nucleic Acids Res Date: 2004-01-01 Impact factor: 16.971