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Web Tools for Rice Transcriptome Analyses

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Abstract

Gene expression databases provide profiling data for the expression of thousands of genes to researchers worldwide. Oligonucleotide microarray technology is a useful tool that has been employed to produce gene expression profiles in most species. In rice, there are five genome-wide DNA microarray platforms: NSF 45K, BGI/Yale 60K, Affymetrix, Agilent Rice 44K, and NimbleGen 390K. Presently, more than 1,700 hybridizations of microarray gene expression data are available from public microarray depositing databases such as NCBI gene expression omnibus and Arrayexpress at EBI. More processing or reformatting of public gene expression data is required for further applications or analyses. Web-based databases for expression meta-analyses are useful for guiding researchers in designing relevant research schemes. In this review, we summarize various databases for expression meta-analyses of rice genes and web tools for further applications, such as the development of co-expression network or functional gene network.

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References

  • Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Edgar R (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 37:D885–D890

    Article  PubMed  CAS  Google Scholar 

  • Ding X, Richter T, Chen M, Fujii H, Seo YS, Xie M, Zheng X, Kanrar S, Stevenson RA, Dardick C, Li Y, Jiang H, Zhang Y, Yu F, Bartley LE, Chern M, Bart R, Chen X, Zhu L, Farmerie WG, Gribskov M, Zhu JK, Fromm ME, Ronald PC, Song WY (2009) A rice kinase–protein interaction map. Plant Physiol 149:1478–1492

    Article  PubMed  CAS  Google Scholar 

  • Ficklin SP, Luo F, Feltus FA (2010) The association of multiple interacting genes with specific phenotypes in rice using gene coexpression networks. Plant Physiol 154:13–24

    Article  PubMed  CAS  Google Scholar 

  • Guldener U, Seong KY, Boddu J, Cho S, Trail F, Xu JR, Adam G, Mewes HW, Muehlbauer GJ, Kistler HC (2006) Development of a Fusarium graminearum Affymetrix GeneChip for profiling fungal gene expression in vitro and in planta. Fungal Genet Biol 43:316–325

    Article  PubMed  Google Scholar 

  • Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, Oertle L, Widmayer P, Gruissem W, Zimmermann P (2008) Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics 2008:420747

    PubMed  Google Scholar 

  • Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AK, Khurana JP (2007) F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiol 143:1467–1483

    Article  PubMed  CAS  Google Scholar 

  • Jung KH, An G, Ronald PC (2008a) Towards a better bowl of rice: assigning function to tens of thousands of rice genes. Nat rev 9:91–101

    CAS  Google Scholar 

  • Jung KH, Dardick C, Bartley LE, Cao P, Phetsom J, Canlas P, Seo YS, Shultz M, Ouyang S, Yuan Q, Frank BC, Ly E, Zheng L, Jia Y, Hsia AP, An K, Chou HH, Rocke D, Lee GC, Schnable PS, An G, Buell CR, Ronald PC (2008b) Refinement of light-responsive transcript lists using rice oligonucleotide arrays: evaluation of gene-redundancy. PLoS ONE 3:e3337

    Article  PubMed  Google Scholar 

  • Jung KH, Lee J, Dardick C, Seo YS, Cao P, Canlas P, Phetsom J, Xu X, Ouyang S, An K, Cho YJ, Lee GC, Lee Y, An G, Ronald PC (2008c) Identification and functional analysis of light-responsive unique genes and gene family members in rice. PLoS Genet 4:e1000164

    Article  PubMed  Google Scholar 

  • Jung KH, Seo YS, Walia H, Cao P, Fukao T, Canlas PE, Amonpant F, Bailey-Serres J, Ronald PC (2010a) The submergence tolerance regulator Sub1A mediates stress-responsive expression of AP2/ERF transcription factors. Plant Physiol 152:1674–1692

    Article  PubMed  CAS  Google Scholar 

  • Jung KH, Cao P, Seo YS, Dardick C, Ronald PC (2010b) The Rice Kinase Phylogenomics Database: a guide for systematic analysis of the rice kinase super-family. Trends Plant Sci 15:595–599

    Article  PubMed  CAS  Google Scholar 

  • Kind T, Scholz M, Fiehn O (2009) How large is the metabolome? A critical analysis of data exchange practices in chemistry. PLoS ONE 4:e5440

    Article  PubMed  Google Scholar 

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, Coulson R, Farne A, Holloway E, Kolesnykov N, Lilja P, Lukk M, Mani R, Rayner T, Sharma A, William E, Sarkans U, Brazma A (2007) ArrayExpress—a public database of microarray experiments and gene expression profiles. Nucleic Acids Res 35:D747–D750

    Article  PubMed  CAS  Google Scholar 

  • Sato Y, Antonio BA, Namiki N, Takehisa H, Minami H, Kamatsuki K, Sugimoto K, Shimizu Y, Hirochika H, Nagamura Y (2011) RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions. Nucleic Acids Res 39:D1141–D1148

    Google Scholar 

  • 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:e718

    Article  PubMed  Google Scholar 

  • Wise RP, Caldo RA, Hong L, Shen L, Cannon E, Dickerson JA (2007) BarleyBase/PLEXdb. Methods Mol Biol 406:347–363

    Article  PubMed  CAS  Google Scholar 

  • Yano K, Imai K, Shimizu A, Hanashita T (2006) A new method for gene discovery in large-scale microarray data. Nucleic Acids Res 34:1532–1539

    Google Scholar 

  • Zheng Q, Wang XJ (2008) GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res 36:W358–W363

    Article  PubMed  CAS  Google Scholar 

  • Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 136:2621–2632

    Article  PubMed  CAS  Google Scholar 

  • Zimmermann P, Laule O, Schmitz J, Hruz T, Bleuler S, Gruissem W (2008) Genevestigator transcriptome meta-analysis and biomarker search using rice and barley gene expression databases. Mol Plant 1:851–857

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We greatly thank Dr. Laura E. Bartley for providing helpful comments and Dr. Pamela C. Ronald for continuous support for developing systems biology in rice. This work was supported by the Mid-career Researcher Program through the National Research Foundation of Korea (NRF) grant funded by the Ministry of Education, Science and Technology (MEST) (2010-0026679) to K.H.J. and J.S.J.

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Authors and Affiliations

  1. Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, South Korea

    Ki-Hong Jung, Jong-Seong Jeon & Gynheung An

  2. Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin, 446-701, South Korea

    Ki-Hong Jung, Jong-Seong Jeon & Gynheung An

  3. Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, South Korea

    Jong-Seong Jeon

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  1. Ki-Hong Jung
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Correspondence to Ki-Hong Jung.

Electronic Supplementary Materials

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Figure S1

Leaf expression pattern analyses of LOC_Os04g09390 gene using RiceXPro. List and growth condition for “Leaf gene expression profile throughout entire growth in the field” are described with links at http://ricexpro.dna.affrc.go.jp/RXP_0003/sample-list.php and http://ricexpro.dna.affrc.go.jp/growth-condition.html. The probes for Agilent Rice 4X44K microarray which is used for the development of this webtool is detailed at http://ricexpro.dna.affrc.go.jp/rice-44k-microarray.html (EPS 4,608 kb)

Figure S1

Low resolution image (JPEG 1,015 kb)

Figure S2

GO enrichment analysis in the cellular component category of genes up-regulated in response to drought using GOEAST (EPS 1,529 kb)

Figure S2

Low resolution image (JPEG 413 kb)

Figure S3

Procedure to identify Affymetrix probe id required to develop co-expression network of LOC_Os02g02410 in Fig. 10 with MSU id (PDF 176 kb)

Figure S4

Screenshots of all additional information about co-expression network of Os.1311.1.S1_at (LOC_Os02g02410) in Fig. 10 (PDF 850 kb)

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Jung, KH., Jeon, JS. & An, G. Web Tools for Rice Transcriptome Analyses. J. Plant Biol. 54, 65–80 (2011). https://doi.org/10.1007/s12374-011-9146-y

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  • DOI: https://doi.org/10.1007/s12374-011-9146-y

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