Abstract
Bioinformatic tools are an increasingly important resource for Arabidopsis researchers. With them, it is possible to rapidly query the large data sets covering genomes, transcriptomes, proteomes, epigenomes, and other “omes” that have been generated in the past decade. Often these tools can be used to generate quality hypotheses at the click of a mouse. In this chapter, we cover the use of bioinformatic tools for examining gene expression and coexpression patterns, performing promoter analyses, looking for functional classification enrichment for sets of genes, and investigating protein–protein interactions. We also introduce bioinformatic tools that allow integration of data from several sources for improved hypothesis generation.
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References
Chory J et al (2000) National Science Foundation-sponsored workshop report: “The 2010 Project” functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them. Plant Physiol 123:423–426
Alonso JM et al (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653–657
Rhee S 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
Finkelstein RR, Somerville CR (1990) Three classes of abscisic acid (ABA)—insensitive mutations of arabidopsis define genes that control overlapping subsets of ABA responses. Plant Physiol 94:1172
Brady S, Provart N (2009) Web-queryable large-scale data sets for hypothesis generation in plant biology. Plant Cell 21:1034
Usadel B et al (2009) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ 32:1633–1651
Winter D et al (2007) An ‘Electronic Fluorescent Pictograph’ browser for exploring and analyzing large-scale biological data sets. PLoS One 2:e718
Hruz T et al (2008) Genevestigator V3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics 420747
O’Connor TR, Dyreson C, Wyrick JJ (2005) Athena: a resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences. Bioinformatics 21:4411–4413
Obayashi T et al (2011) ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. Plant Cell Physiol 52:213–219
Toufighi K et al (2005) The botany array resource: e-Northerns, expression angling, and promoter analyses. Plant J 43:153–163
Du Z et al (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38:W64–W70
Carbon S et al (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25:288–289
Provart N, Zhu T (2003) A browser-based functional classification SuperViewer for Arabidopsis genomics. Curr Comput Mol Biol 2003:271–272
Mueller LA, Zhang P, Rhee SY (2003) AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol 132:453–460
Thimm O et al (2004) Mapman: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J 37:914–939
Heazlewood JL et al (2007) SUBA: the Arabidopsis subcellular database. Nucleic Acids Res 35:D213–D218
Geisler-Lee J et al (2007) A predicted interactome for Arabidopsis. Plant Physiol 145(2):317–329
Katari MS et al (2010) VirtualPlant: a software platform to support systems biology research. Plant Physiol 152:500–515
Mostafavi S et al (2008) GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol 9(Suppl 1):S4
Fucile G et al (2011) ePlant and the 3D data display initiative: integrative systems biology on the World Wide Web. PLoS One 6:e15237
Mu J et al (2008) LEAFY COTYLEDON1 is a key regulator of fatty acid biosynthesis in Arabidopsis. Plant Physiol 148:1042–1054
Schmid M et al (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37:501–506
Nakabayashi K et al (2005) Genome wide profiling of stored mRNA in Arabidopsis thaliana seed germination: epigenetic and genetic regulation of transcription in seed. Plant J 41:697–709
Brady SM et al (2003) The ABSCISIC ACID INSENSITIVE 3 (ABI3) gene is modulated by farnesylation and is involved in auxin signaling and lateral root development in Arabidopsis. Plant J 34:67–75
Laubinger S et al (2008) At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Genome Biol 9:R112
Zeller G et al (2009) Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. Plant J 58:1068–1082
Brady SM et al (2007) A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 318:801–806
Obayashi T, Kinoshita K (2009) Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. DNA Res 16:249–260
Dubreucq B et al (2000) The Arabidopsis AtEPR1 extensin-like gene is specifically expressed in endosperm during seed germination. Plant J 23:643–652
Nole-Wilson S, Tranby TL, Krizek BA (2005) AINTEGUMENTA-like (AIL) genes are expressed in young tissues and may specify meristematic or division-competent states. Plant Mol Biol 57:613–628
Chattopadhyay S et al (1998) Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression. The Plant Cell Online 10:673–684
Higo K et al (1999) Plant cis-acting regulatory DNA elements (PLACE) database: 1999. Nucleic Acids Res 27:297–300
Liu B, Chen J, Shen B (2011) Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs. BMC Syst Biol 5:S2
Ouyang X et al (2011) Genome-wide binding site analysis of FAR-RED ELONGATED HYPOCOTYL3 reveals its novel function in Arabidopsis development. The Plant Cell Online 23:2514–2535
Zhang H et al (2011) Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulation. Plant J 65:346–358
Razem FA et al (2006) The RNA-binding protein FCA is an abscisic acid receptor. Nature 439:290–294
Ashburner M et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29
Baud S et al (2002) An integrated overview of seed development in Arabidopsis thaliana ecotype WS. Plant Physiol Biochem 40:151–160
Hua S, Sun Z (2001) Support vector machine approach for protein subcellular localization prediction. Bioinformatics 17:721–728
Horton P et al (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35:W585–W587
Aranda B et al (2009) The IntAct molecular interaction database in 2010. Nucleic Acids Res 38:D525–D531
Stark C et al (2011) The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 39:D698–D704
Li P et al (2011) AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis. Nucleic Acids Res 39:D1130–D1133
Klopffleisch K et al (2011) Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis. Mol Syst Biol 7
Nakamura S, Lynch TJ, Finkelstein RR (2001) Physical interactions between ABA response loci of Arabidopsis. Plant J 26:627–635
Cui H et al (2007) An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants. Science 316:421–425
De Lucas M et al (2008) A molecular framework for light and gibberellin control of cell elongation. Nature 451:480–484
Dill A, Jung HS, Sun T (2001) The DELLA motif is essential for gibberellin-induced degradation of RGA. Proc Natl Acad Sci 98:14162
Nordborg M et al (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol 3:e196
Choi H (2000) ABFs, a family of ABA-responsive element binding factors. J Biol Chem 275:1723–1730
Eden E et al (2009) GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10:48
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de Lucas, M., Provart, N.J., Brady, S.M. (2014). Bioinformatic Tools in Arabidopsis Research. In: Sanchez-Serrano, J., Salinas, J. (eds) Arabidopsis Protocols. Methods in Molecular Biology, vol 1062. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-580-4_5
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DOI: https://doi.org/10.1007/978-1-62703-580-4_5
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