Abstract
Gene coexpression analyses are a powerful method to predict the function of genes and/or to identify genes that are functionally related to query genes. The basic idea of gene coexpression analyses is that genes with similar functions should have similar expression patterns under many different conditions. This approach is now widely used by many experimental researchers, especially in the field of plant biology. In this review, we will summarize recent successful examples obtained by using our gene coexpression database, ATTED-II. Specifically, the examples will describe the identification of new genes, such as the subunits of a complex protein, the enzymes in a metabolic pathway and transporters. In addition, we will discuss the discovery of a new intercellular signaling factor and new regulatory relationships between transcription factors and their target genes. In ATTED-II, we provide two basic views of gene coexpression, a gene list view and a gene network view, which can be used as guide gene approach and narrow-down approach, respectively. In addition, we will discuss the coexpression effectiveness for various types of gene sets.
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Akiyama K, Chikayama E, Yuasa H, Shimada Y, Tohge T, Shinozaki K, Hirai MY, Sakurai T, Kikuchi J, Saito K (2008) PRIMe: a Web site that assembles tools for metabolomics and transcriptomics. In Silico Biol 8:339–345
Anderson PW (1972) More is different. Science 177:393–396
Aoki K, Ogata Y, Shibata D (2007) Approaches for extracting practical information from gene co-expression networks in plant biology. Plant Cell Physiol 48:381–390
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29
Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R (2007) NCBI GEO: mining tens of millions of expression profiles—database and tools update. Nucleic Acids Res 35:D760–D765
Batagelj V, Mrvar A (1998) Pajek program for large network analysis. Connections 21:47–57
Bednarek P, Pislewska-Bednarek M, Svatos A, Schneider B, Doubsky J, Mansurova M, Humphry M, Consonni C, Panstruga R, Sanchez-Vallet A, Molina A, Schulze-Lefert P (2009) A glucosinolate metabolism pathway in living plant cells mediates broad-spectrum antifungal defense. Science 323:101–106
Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2:2366–2382
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–D577
Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95:14863–14868
Hirai MY, Sugiyama K, Sawada Y, Tohge T, Obayashi T, Suzuki A, Araki R, Sakurai N, Suzuki H, Aoki K, Goda H, Nishizawa OI, Shibata D, Saito K (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Natl Acad Sci USA 104:6478–6483
Ishihara S, Takabayashi A, Ido K, Endo T, Ifuku K, Sato F (2007) Distinct functions for the two PsbP-like proteins PPL1 and PPL2 in the chloroplast thylakoid lumen of Arabidopsis. Plant Physiol 145:668–679
Ishikawa N, Takabayashi A, Ishida S, Hano Y, Endo T, Sato F (2008) NDF6: a thylakoid protein specific to terrestrial plants is essential for activity of chloroplastic NAD(P)H dehydrogenase in Arabidopsis. Plant Cell Physiol 49:1066–1073
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–484
Kinoshita K, Obayashi T (2009) Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis. Bioinformatics 25:2677–2684
Lee TH, Kim YK, Pham TT, Song SI, Kim JK, Kang KY, An G, Jung KH, Galbraith DW, Kim M, Yoon UH, Nahm BH (2009) RiceArrayNet: a database for correlating gene expression from transcriptome profiling, and its application to the analysis of coexpressed genes in rice. Plant Physiol 151:16–33
Lysenko A, Hindle MM, Taubert J, Saqi M, Rawlings CJ (2009) Data integration for plant genomics—exemplars from the integration of Arabidopsis thaliana databases. Brief Bioinform 10:676–693
Manfield IW, Jen C-H, Pinney JW, Michalopoulos I, Bradford JR, Gilmartin PM, Westhead DR (2006) Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. Nucleic Acids Res 34:W504–W509
Masuda T, Fujita Y (2008) Regulation and evolution of chlorophyll metabolism. Photochem Photobiol Sci 7:1131–1149
Mutwil M, Obro J, Willats WGT, Persson S (2008) GeneCAT—novel webtools that combine BLAST and co-expression analyses. Nucleic Acids Res 36:W320–W326
Obayashi T, Kinoshita K (2009) Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. DNA Res 16:249–260
Obayashi T, Okegawa T, Sasaki-Sekimoto Y, Shimada H, Masuda T, Asamizu E, Nakamura Y, Shibata D, Tabata S, Takamiya K, Ohta H (2004) Distinctive features of plant organs characterized by global analysis of gene expression in Arabidopsis. DNA Res 11:11–25
Obayashi T, Kinoshita K, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta H (2007) ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res 35:D863–D869
Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, Kinoshita K (2008) COXPRESdb: a database of coexpressed gene networks in mammals. Nucleic Acids Res 36:D77–D82
Obayashi T, Hayashi S, Saeki M, Ohta H, Kinoshita K (2009) ATTED-II provides coexpressed gene networks for Arabidopsis. Nucleic Acids Res 37:D987–D991
Ogata Y, Suzuki H, Shibata D (2009a) A gene co-expression database for understanding biological process in soybean. Plant Biotechnol 26:503–507
Ogata Y, Suzuki H, Shibata D (2009b) A database for poplar gene co-expression analysis for systematic understanding of biological processes, including stress responses. J Wood Sci 55:395–400
Okazaki Y, Shimojima M, Sawada Y, Toyooka K, Narisawa T, Mochida K, Tanaka H, Matsuda F, Hirai A, Hirai MY, Ohta H, Saito K (2009) A chloroplastic UDP-glucose pyrophosphorylase from Arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis. Plant Cell 21:892–909
Pitzschke A, Hirt H (2010) Bioinformatic and systems biology tools to generate testable models of signaling pathways and their targets. Plant Physiol 152:460–469
Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S, Vilo J, Abeygunawardena N, Mukherjee G, Holloway E, Kapushesky M, Kemmeren P, Lara GG, Oezcimen A, Sansone SA (2003) ArrayExpress: a public database of gene expression data at EBI. C R Biol 326:1075–1078
Saito K, Hirai MY, Yonekura-Sakakibara K (2008) Decoding genes with coexpression networks and metabolomics—‘majority report by precogs’. Trends Plant Sci 13:36–43
Sano R, Ogata Y, Suzuki H, Ogawa Y, Dansako T, Sakurai N, Okazaki K, Aoki K, Saito K, Shibata D (2008) Over-expression of transcription associated factor genes coexpressed with genes of the mevalonate pathway, upstream of isoprenoid biosynthesis, in Arabidopsis cultured cells. Plant Biotechnol 25:583–587
Sawada Y, Kuwahara A, Nagano M, Narisawa T, Sakata A, Saito K, Hirai MY (2009a) Omics-based approaches to methionine side chain elongation in Arabidopsis: characterization of the genes encoding methylthioalkylmalate isomerase and methylthioalkylmalate dehydrogenase. Plant Cell Physiol 50:1181–1190
Sawada Y, Toyooka K, Kuwahara A, Sakata A, Nagano M, Saito K, Hirai MY (2009b) Arabidopsis bile acid: sodium symporter family protein 5 is involved in methionine-derived glucosinolate biosynthesis. Plant Cell Physiol 50:1579–1586
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37:501–506
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
Steinhauser D, Usadel B, Luedemann A, Thimm O, Kopka J (2004) CSB.DB: a comprehensive systems-biology database. Bioinformatics 20:3647–3651
Sugano SS, Shimada T, Imai Y, Okawa K, Tamai A, Mori M, Hara-Nishimura I (2010) Stomagen positively regulates stomatal density in Arabidopsis. Nature 463:241–244
Swarbreck D, Wilks C, Lamesch P, Berardini TZ, Garcia-Hernandez M, Foerster H, Li D, Meyer T, Muller R, Ploetz L, Radenbaugh A, Singh S, Swing V, Tissier C, Zhang P, Huala E (2008) The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res 36:D1009–D1014
Takabayashi A, Ishikawa N, Obayashi T, Ishida S, Obokata J, Endo T, Sato F (2009) Three novel subunits of Arabidopsis chloroplastic NAD(P)H dehydrogenase identified by bioinformatic and reverse genetic approaches. Plant J 57:207–219
Takahashi N, Lammens T, Boudolf V, Maes S, Yoshizumi T, De Jaeger G, Witters E, Inze D, De Veylder L (2008) The DNA replication checkpoint aids survival of plants deficient in the novel replisome factor ETG1. EMBO J 27:1840–1851
Tohge T, Yonekura-Sakakibara K, Niida R, Watanabe-Takahashi A, Saito K (2007) Phytochemical genomics in Arabidopsis thaliana: a case study for functional identification of flavonoid biosynthesis genes. Pure Apple Chem 79:811–823
Tokimatsu T, Sakurai N, Suzuki H, Ohta H, Nishitani K, Koyama T, Umezawa T, Misawa N, Saito K, Shibata D (2005) KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps. Plant Physiol 138:1289–1300
Toufighi K, Brady M, Austin R, Ly E, Provart N (2005) The botany array resource: e-northerns, expression angling, and promoter analyses. Plant J 43:153–163
Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ (2009) Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ 32:1633–1651
Vicinanza M, D’Angelo G, Di Campli A, De Matteis MA (2008) Function and dysfunction of the PI system in membrane trafficking. EMBO J 27:2457–2470
Yamada K, Nagano AJ, Nishina M, Hara-Nishimura I, Nishimura M (2008) NAI2 is an endoplasmic reticulum body component that enables ER body formation in Arabidopsis thaliana. Plant Cell 20:2529–2540
Yonekura-Sakakibara K, Tohge T, Niida R, Saito K (2007) Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression analysis and reverse genetics. J Biol Chem 282:14932–14941
Yonekura-Sakakibara K, Tohge T, Matsuda F, Nakabayashi R, Takayama H, Niida R, Watanabe-Takahashi A, Inoue E, Saito K (2008) Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis. Plant Cell 20:2160–2176
Yoshida Y, Makita Y, Heida N, Asano S, Matsushima A, Ishii M, Mochizuki Y, Masuya H, Wakana S, Kobayashi N, Toyoda T (2009) PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning. Nucleic Acids Res 37:W147–W152
Acknowledgments
This work was supported by a Grant-in-Aid for Scientific Research (No. 50397048) to TO and a Grant-in-Aid for Scientific Research on Priority Areas “Transportsome” to KK. Computation time was provided by the Super Computer System, Human Genome Center, Institute of Medical Science, The University of Tokyo.
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Takeshi Obayashi is the recipient of the BSJ Special Award, 2009.
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Obayashi, T., Kinoshita, K. Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways. J Plant Res 123, 311–319 (2010). https://doi.org/10.1007/s10265-010-0333-6
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DOI: https://doi.org/10.1007/s10265-010-0333-6