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Arabidopsis Database and Stock Resources

  • Donghui Li
  • Kate Dreher
  • Emma Knee
  • Jelena Brkljacic
  • Erich Grotewold
  • Tanya Z. Berardini
  • Philippe Lamesch
  • Margarita Garcia-Hernandez
  • Leonore Reiser
  • Eva Huala
Part of the Methods in Molecular Biology book series (MIMB, volume 1062)

Abstract

The volume of Arabidopsis information has increased enormously in recent years as a result of the sequencing of the reference genome and other large-scale functional genomics projects. Much of the data is stored in public databases, where data are organized, analyzed, and made freely accessible to the research community. These databases are resources that researchers can utilize for making predictions and developing testable hypotheses. The methods in this chapter describe ways to access and utilize Arabidopsis data and genomic resources found in databases and stock centers.

Key words

Data mining Database Genomics Gene expression Bioinformatics Computational biology Stocks Arabidopsis thaliana 

Notes

Acknowledgements

This project was supported by the National Science Foundation (grant number DBI-0850219, DBI-0640769, IOS-1026003), the National Institute of Health National Human Genome Research Institute (NIH-NHGRI) (grant number 5P41HG002273-09), and the TAIR sponsorship program (http://www.arabidopsis.org/doc/about/tair_sponsors/413).

References

  1. 1.
    Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815CrossRefGoogle Scholar
  2. 2.
    The Multinational Arabidopsis Steering Committee (2011) The multinational coordinated Arabidopsis thaliana functional genomics project annual report 2011. http://www.arabidopsis.org/portals/masc/2011_MASC_Report.pdf
  3. 3.
    Alonso JM, Stepanova AN, Leisse TJ et al (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653–657PubMedCrossRefGoogle Scholar
  4. 4.
    Garcia-Hernandez M, Berardini TZ, Chen G et al (2002) TAIR: a resource for integrated Arabidopsis data. Funct Integr Genomics 2:239–253PubMedCrossRefGoogle Scholar
  5. 5.
    Huala E, Dickerman AW, Garcia-Hernandez M et al (2001) The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res 29:102–105PubMedCrossRefGoogle Scholar
  6. 6.
    Rhee SY, Beavis W, Berardini TZ et al (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31:224–228PubMedCrossRefGoogle Scholar
  7. 7.
    Swarbreck D, Wilks C, Lamesch P et al (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 36:D1009–D1014PubMedCrossRefGoogle Scholar
  8. 8.
    Lamesch P, Berardini TZ, Li D et al (2011) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. doi: 10.1093/nar/gkr1090 PubMedGoogle Scholar
  9. 9.
    Meinke D, Scholl R (2003) The preservation of plant genetic resources: experiences with Arabidopsis. Plant Physiol 133:1046–1050PubMedCrossRefGoogle Scholar
  10. 10.
    Heazlewood JL, Verboom RE, Tonti-Filippini J et al (2007) SUBA: the Arabidopsis subcellular database. Nucleic Acids Res 35:D213–D218PubMedCrossRefGoogle Scholar
  11. 11.
    Lu Y, Savage LJ, Larson M et al (2011) Chloroplast 2010: a database for large-scale phenotypic screening of Arabidopsis mutants. Plant Physiol 155:1589–1900PubMedCrossRefGoogle Scholar
  12. 12.
    International Arabidopsis Informatics Consortium (2010) An international bioinformatics infrastructure to underpin the Arabidopsis community. Plant Cell 22:2530–2536CrossRefGoogle Scholar
  13. 13.
    Samson F, Brunaud V, Balzergue S et al (2002) FLAGdb/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants. Nucleic Acids Res 30:94–97PubMedCrossRefGoogle Scholar
  14. 14.
    Kleinboelting N, Huep G, Kloetgen A et al (2011) GABI-Kat Simple Search: new features of the Arabidopsis thaliana T-DNA mutant database. Nucleic Acids Res. doi: 10.1093/nar/gkr1047 PubMedGoogle Scholar
  15. 15.
    Lamesch P, Dreher K, Swarbreck D, et al. (2010) Using the Arabidopsis Information Resource (TAIR) to find information about Arabidopsis genes. Curr Protoc Bioinformatics. Chapter 1:Unit1.11Google Scholar
  16. 16.
    Craigon DJ, James N, Okyere J, Higgins J et al (2004) A repository for microarray data generated by NASC’s transcriptomics service. Nucleic Acids Res 32:D575–D577PubMedCrossRefGoogle Scholar
  17. 17.
    Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29PubMedCrossRefGoogle Scholar
  18. 18.
    Jaiswal P, Avraham S, Ilic K et al (2005) Plant ontology (PO): a controlled vocabulary of plant structures and growth stages. Comp Funct Genomics 6:388–397PubMedCrossRefGoogle Scholar
  19. 19.
    Reference Genome Group of the Gene Ontology Consortium (2009) The Gene Ontology’s Reference Genome project: a unified framework for functional annotation across species. PLoS Comput Biol 5:e1000431CrossRefGoogle Scholar
  20. 20.
    Ort DR, Grennan AK (2008) Plant physiology and TAIR partnership. Plant Physiol 146:1022–1023PubMedCrossRefGoogle Scholar
  21. 21.
    Cutler S, Ghassemian M, Bonetta D et al (1996) A protein farnesyl transferase involved in abscisic acid signal transduction in Arabidopsis. Science 273:1239–1241PubMedCrossRefGoogle Scholar
  22. 22.
    Yalovsky S, Kulukian A, Rodriguez-Concepcion M et al (2000) Functional requirement of plant farnesyltransferase during development in Arabidopsis. Plant Cell 12:1267–1278PubMedGoogle Scholar
  23. 23.
    Ziegelhoffer EC, Medrano LJ, Meyerowitz EM (2000) Cloning of the Arabidopsis WIGGUM gene identifies a role for farnesylation in meristem development. Proc Natl Acad Sci USA 97:7633–7638PubMedCrossRefGoogle Scholar
  24. 24.
    Schmid M, Davison TS, Henz SR et al (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37:501–506PubMedCrossRefGoogle Scholar
  25. 25.
    Parkinson H, Sarkans U, Kolesnikov N et al (2011) ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res 39:D1002–1004PubMedCrossRefGoogle Scholar
  26. 26.
    Barrett T, Troup DB, Wilhite SE et al (2011) NCBI GEO: archive for functional genomics data sets—10 years on. Nucleic Acids Res 39:D1005–1010PubMedCrossRefGoogle Scholar
  27. 27.
    Hruz T, Laule O, Szabo G et al (2008) Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics 2008:420747PubMedGoogle Scholar
  28. 28.
    Winter D, Vinegar B, Nahal H et al (2007) An “electronic fluorescent pictograph” browser for exploring and analyzing large-scale biological data sets. PLoS One 2:e718. doi: 10.1371/journal.pone.0000718 PubMedCrossRefGoogle Scholar
  29. 29.
    Zhang P, Dreher K, Karthikeyan A et al (2010) Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiol 153:1479–1491PubMedCrossRefGoogle Scholar
  30. 30.
    Tsesmetzis N, Couchman M, Higgins J et al (2008) Arabidopsis reactome: a foundation knowledgebase for plant systems biology. Plant Cell 20:1426–1436PubMedCrossRefGoogle Scholar
  31. 31.
    Masoudi-Nejad A, Goto S, Endo TR et al (2007) KEGG bioinformatics resource for plant genomics research. Methods Mol Biol 406:437–458PubMedGoogle Scholar
  32. 32.
    Sakurai N, Ara T, Ogata Y et al (2011) KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. Nucleic Acids Res 39:D677–684PubMedCrossRefGoogle Scholar
  33. 33.
    Wurtele ES, Li L, Berleant D et al (2007) MetNet: systems biology software for Arabidopsis. In: Nikolau BJ, Wurtele ES (eds) Concepts in plant metabolomics. Springer, Berlin, pp 145–158CrossRefGoogle Scholar
  34. 34.
    Grafahrend-Belau E, Weise S, Koschützki D et al (2008) MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Res 36:D954–958PubMedCrossRefGoogle Scholar
  35. 35.
    Shinbo Y, Nakamura Y, Altaf-Ul-Amin M et al (2006) KNApSAcK: A comprehensive species-metabolite relationship database. In: Saito K, Dixon RA, Willmitzer L (ed) Plant metabolomics. Berlin, Springer, pp 165–181. doi:  10.1007/3-540-29782-0_13
  36. 36.
    Karp P, Paley S, Romero P (2002) The pathway tools software. Bioinformatics 18:S225–S232PubMedCrossRefGoogle Scholar
  37. 37.
    Mueller LA, Zhang P, Rhee SY (2003) AraCyc. A biochemical pathway database for Arabidopsis. Plant Physiol 132:453–460PubMedCrossRefGoogle Scholar
  38. 38.
    Zhang P, Foerster H, Tissier C et al (2005) MetaCyc and AraCyc: metabolic pathway databases for plant research. Plant Physiol 138:27–37PubMedCrossRefGoogle Scholar
  39. 39.
    Müller HM, Kenny EE, Sternberg PW (2004) Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol 2:e309PubMedCrossRefGoogle Scholar
  40. 40.
    Rhee SY, Wood V, Dolinski K et al (2008) Use and misuse of the gene ontology annotations. Nat Rev Genet 9:509–515PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Donghui Li
    • 1
  • Kate Dreher
    • 1
  • Emma Knee
    • 2
  • Jelena Brkljacic
    • 2
  • Erich Grotewold
    • 2
  • Tanya Z. Berardini
    • 1
  • Philippe Lamesch
    • 1
  • Margarita Garcia-Hernandez
    • 1
  • Leonore Reiser
    • 1
  • Eva Huala
    • 1
  1. 1.Department of Plant BiologyCarnegie Institution for ScienceStanfordUSA
  2. 2.Arabidopsis Biological Resource CenterThe Ohio State UniversityColumbusUSA

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