Abstract
A number of studies have shown that functionally related genes are often co-expressed and that computational based co-expression analysis can be used to accurately identify functional relationships between genes and by inference, their encoded proteins. Here we describe how a computational based co-expression analysis can be used to link the function of a specific gene of interest to a defined cellular response. Using a worked example we demonstrate how this methodology is used to link the function of the Arabidopsis Wall-Associated Kinase-Like 10 gene, which encodes a functional guanylyl cyclase, to host responses to pathogens.
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References
Newton RP, Smith CJ (2004) Cyclic nucleotides. Phytochemistry 65:2423–2437
Salmi ML, Morris KE, Roux SJ, Porterfield DM (2007) Nitric oxide and cGMP signaling in calcium-dependent development of cell polarity in Ceratopteris richardii. Plant Physiol 144:94–104
Stöhr C, Stremlau S (2006) Formation and possible roles of nitric oxide in plant roots. J Exp Bot 57:463–470
Durner J, Wendehenne D, Klessig DF (1998) Defense gene induction in tobacco by nitric oxide, cyclic GMP, and cyclic ADP-ribose. Proc Natl Acad Sci USA 95:10328–10333
Pasqualini S, Meier S, Gehring C, Madeo L, Fornaciari M et al (2009) Ozone and nitric oxide induce cGMP-dependent and -independent transcription of defence genes in tobacco. New Phytol 181:860–870
Ludidi N, Gehring C (2003) Identification of a novel protein with guanylyl cyclase activity in Arabidopsis thaliana. J Biol Chem 278:6490–6494
Kwezi L, Meier S, Mungur L, Ruzvidzo O, Irving H et al (2007) The Arabidopsis thaliana brassinosteroid receptor (AtBRI1) contains a domain that functions as a guanylyl cyclase in vitro. PLoS One 2:e449
Meier S, Ruzvidzo O, Morse M, Donaldson L, Kwezi L et al (2010) The arabidopsis wall associated kinase-like 10 gene encodes a functional guanylyl cyclase and is co-expressed with pathogen defense related genes. PLoS One 5:e8904
Mulaudzi T, Ludidi N, Ruzvidzo O, Morse M, Hendricks N et al (2011) Identification of a novel Arabidopsis thaliana nitric oxide-binding molecule with guanylate cyclase activity in vitro. FEBS Lett 585:2693–2697
Qi Z, Verma R, Gehring C, Yamaguchi Y, Zhao Y et al (2010) Ca2+ signaling by plant Arabidopsis thaliana pep peptides depends on AtPepR1, a receptor with guanylyl cyclase activity, and cGMP-activated Ca2+ channels. Proc Natl Acad Sci USA 49:21193–21198
Kwezi L, Ruzvidzo O, Wheeler JI, Govender K, Iacuone S et al (2011) The phytosulfokine (PSK) receptor is capable of guanylate cyclase activity and enabling cyclic GMP-dependent signaling in plants. J Biol Chem 286:22580–22588
Allocco D, Kohane I, Butte A (2004) Quantifying the relationship between co-expression, co-regulation and gene function. BMC Bioinformatics 5:18
Jansen R, Greenbaum D, Gerstein M (2002) Relating whole-genome expression data with protein–protein interactions. Genome Res 12:37–46
Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302:249–255
Pandey SP, Somssich IE (2009) The role of WRKY transcription factors in plant immunity. Plant Physiol 150:1648–1655
Manfield IW, Jen C-H, Pinney JW, Michalopoulos I, Bradford JR et al (2006) Arabidopsis co-expression tool (ACT): web server tools for microarray-based gene expression analysis. Nucleic Acids Res 34:W504–W509
Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S et al (2008) Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics 2008:420747
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
Maleck K, Levine A, Eulgem T, Morgan A, Schmid J et al (2000) The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nat Genet 26:403–410
Obayashi T, Nishida K, Kasahara K, Kinoshita K (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
Jung K-H, Dardick C, Bartley LE, Cao P, Phetsom J et al (2008) Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PLoS One 3:e3337
Obayashi T, Kinoshita K (2011) COXPRESdb: a database to compare gene coexpression in seven model animals. Nucleic Acids Res 39:D1016–D1022
Steinhauser D, Usadel B, Luedemann A, Thimm O, Kopka J (2004) CSB.DB: a comprehensive systems-biology database. Bioinformatics 20:3647–3651
Srinivasasainagendra V, Page GP, Mehta T, Coulibaly I, Loraine AE (2008) CressExpress: a tool for large-scale mining of expression data from arabidopsis. Plant Physiol 147:1004–1016
Maere S, Heymans K, Kuiper M (2005) BiNGO: a cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21:3448–3449
Zhou X, Su Z (2007) EasyGO: gene ontology-based annotation and functional enrichment analysis tool for agronomical species. BMC Genomics 8:246
Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B et al (2009) AmiGO: online access to ontology and annotation data. Bioinformatics 25:288–289
Al-Shahrour F, Minguez P, Tárraga J, Medina I, Alloza E et al (2007) FatiGO+: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res 35:W91–W96
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Alqurashi, M., Meier, S. (2013). Inferring Biological Functions of Guanylyl Cyclases with Computational Methods. In: Gehring, C. (eds) Cyclic Nucleotide Signaling in Plants. Methods in Molecular Biology, vol 1016. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-441-8_15
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DOI: https://doi.org/10.1007/978-1-62703-441-8_15
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