Advertisement

Bioinformatics Resources for Arabidopsis thaliana

  • Neil GrahamEmail author
  • Sean May
Chapter
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 9)

Abstract

Arabidopsis thaliana was the first plant to be sequenced in 2000 and is widely used as a model organism for flowering plants. This has led to the generation of large data sets, such as sequences (DNA, RNA and proteins), gene predictions, protein information and microarray data. A number of different databases have been developed to store, distribute and analyse these data. These range from large repositories that contain a wide range of data (e.g. sequences, gene models, germplasm data) and small specialised databases containing one type of data (e.g. protein localisation). In addition tools have been developed to enable users to access, download and analyse the data. These include tools to analyse sequences, gene function, metabolomic pathways and microarray data. A number of these databases and tools will be described.

Keywords

Arabidopsis Transcriptomics Genomics Proteomics Bioinformatics 

References

  1. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815CrossRefGoogle Scholar
  2. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al (2000) Gene ontology: tool for unification of biology. The gene ontology consortium. Nat Genet 25:25–29CrossRefPubMedGoogle Scholar
  3. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evanglista C, Kim IF, Sobleva A, Tomashevsky M, Marshall KA et al (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 37:D885–D890CrossRefPubMedGoogle Scholar
  4. Birnbaum K, Shasha DE, Wang JY, Jung JW, Lambert GM, Galbraith DW, Benfey PN (2003) A gene expression map of the Arabidopsis root. Science 302:1956–1960CrossRefPubMedGoogle Scholar
  5. Brady SM, Orlando DA, Lee Ji Y, Wang JY, Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN (2007) A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318:801–806CrossRefPubMedGoogle Scholar
  6. Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA et al (2007) Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science 317:338–342CrossRefPubMedGoogle Scholar
  7. Craigon DJ, James N, Okyere J, Higgins J, Jotham J, May S (2004) NASCArrays: a repository for microarray data generated by NASC’s transcriptomics service. Nucleic Acids Res 32:D575–D577CrossRefPubMedGoogle Scholar
  8. Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, Shi T (2008) AtPID: Arabidopsis thaliana protein interactome database and integrative platform for systems biology. Nucleic Acids Res 36:D999–D1008CrossRefPubMedGoogle Scholar
  9. Geisler-Lee J, O’Toole N, Ammar R, Provart NJ, Millar AH, Geisler M (2007) A predicted interactome for Arabidopsis. Plant Physiol 145:317–329CrossRefPubMedGoogle Scholar
  10. Heazlewood JL, Verboom RE, Tonti-Filippinin J, Small I, Millar AH (2007) SUBA: the Arabidopsis subcellular database. Nucleic Acids Res 35:D213–D218CrossRefPubMedGoogle Scholar
  11. Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmerman P (2008) Genevestigator V3: a reference expression database for meta-analysis of transcriptomes. Adv Bioinformatics 2008:420747PubMedGoogle Scholar
  12. James N, Graham N, Clemects D, Schildknecht B, May S (2007) AtEnsembl – a post genomic resources browser for Arabidopsis. In: Edwards D (ed) Plant bioinformatics – methods and protocols, Humana Press. ISBN10:1-58829-653-9Google Scholar
  13. Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A et al (2008) Gramene: a growing plant comparative genomics resource. Nucleic Acids Res 36:D947–D953CrossRefPubMedGoogle Scholar
  14. Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, Carver T, Glover K, Pocock MR, Wipat A, Li P (2004) Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 20:3045–3054CrossRefPubMedGoogle Scholar
  15. Parkinson H, Kapushesky M, Kolenikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A et al (2009) ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 37:D868–D872CrossRefPubMedGoogle Scholar
  16. Rombauts S, dehais P, Van Montagu M, Rouze P (1999) PlantCARE, a plant cis-acting regulatory element database. Nucleic Acids Res 27:295–296CrossRefPubMedGoogle Scholar
  17. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S (2002) The generic genome browser: a building block for model organism system database. Genome Res 12:1599–1610CrossRefPubMedGoogle Scholar
  18. Thimm O, Blaesing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets on diagrams of metabolic pathways and other biological processes. Plant J 37:914–939CrossRefPubMedGoogle Scholar
  19. Tsesmetzis N, Couchman M, Higgins J, Smith A, Doonan JH, Seifert GJ, Schmidt EE, Vastrik I, Birney E, Wu GM et al (2008) Arabidopsis reactome: a foundation knowledgebase for plant systems biology. Plant Cell 20:1426–1436CrossRefPubMedGoogle Scholar
  20. Winter D, Vinegar B, Nahal H, Ammar R, Wilson GV, Provart NJ (2007) An “electronic fluorescent pictograph” browser for exploring and analyzing large-scale biological data sets. PLoS ONE 2:e718CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Plant and Crop Sciences DivisionNottingham Arabidopsis Stock Centre, University of NottinghamLoughboroughUK

Personalised recommendations