The Rice Oligonucleotide Array Database: an atlas of rice gene expression

Cao, Peijian; Jung, Ki-Hong; Choi, Daeseok; Hwang, Daehee; Zhu, Jun; Ronald, Pamela C.

doi:10.1186/1939-8433-5-17

Title: The Rice Oligonucleotide Array Database: an atlas of rice gene expression

Journal Article · Thu Jul 19 00:00:00 EDT 2012 · Rice

DOI:https://doi.org/10.1186/1939-8433-5-17· OSTI ID:1626665

Cao, Peijian ^[1]; Jung, Ki-Hong ^[2]; Choi, Daeseok ^[3]; Hwang, Daehee ^[3]; Zhu, Jun ^[1]; Ronald, Pamela C. ^[4]

Zhejiang University, Hangzhou (China)
Kyung Hee University Yongin (Korea, Republic of)
Pohang University of Science and Technology (POSTECH) (Korea, Republic of)
Kyung Hee University Yongin (Korea, Republic of); University of California, Davis, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States)

Microarray technologies facilitate high-throughput gene expression analysis. However, the diversity of platforms for rice gene expression analysis hinders efficient analysis. Tools to broadly integrate microarray data from different platforms are needed. In this study, we developed the Rice Oligonucleotide Array Database (ROAD, http://www.ricearray.org) to explore gene expression across 1,867 publicly available rice microarray hybridizations. The ROAD’s user-friendly web interface and variety of visualization tools facilitate the extraction of gene expression profiles using gene and microarray element identifications. The ROAD supports meta-analysis of genes expressed in different tissues and at developmental stages. Co-expression analysis tool provides information on co-regulation between genes under general, abiotic and biotic stress conditions. Additionally, functional analysis tools, such as Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology, are embedded in the ROAD. These tools facilitate the identification of meaningful biological patterns in a list of query genes. The Rice Oligonucleotide Array Database provides comprehensive gene expression profiles for all rice genes, and will be a useful resource for researchers of rice and other grass species.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Basic Research Program of China; Next-Generation BioGreen 21 Program

Grant/Contract Number:: AC02-05CH11231; 2011CB109306; PJ008079; PJ008173; 20080401

OSTI ID:: 1626665

Journal Information:: Rice, Vol. 5, Issue 1; ISSN 1939-8433

Publisher:: SpringerOpenCopyright Statement

Country of Publication:: United States

Language:: English

References (52)

Cytoplasmic–Nuclear Genomic Barriers in Rice Pollen Development Revealed by Comparison of Global Gene Expression Profiles among Five Independent Cytoplasmic Male Sterile Lines Fujii, Sota; Yamada, Mari; Fujita, Masahiro Plant and Cell Physiology, Vol. 51, Issue 4 https://doi.org/10.1093/pcp/pcq026	journal	April 2010
PLEXdb: gene expression resources for plants and plant pathogens Dash, S.; Van Hemert, J.; Hong, L. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr938	journal	November 2011
The Gene Ontology project in 2008 Nucleic Acids Research, Vol. 36, Issue suppl_1, p. D440-D444 https://doi.org/10.1093/nar/gkm883	journal	November 2007
The Institute for Genomic Research Osa1 Rice Genome Annotation Database Yuan, Qiaoping; Ouyang, Shu; Wang, Aihui Plant Physiology, Vol. 138, Issue 1 https://doi.org/10.1104/pp.104.059063	journal	May 2005
ArrayExpress--a public database of microarray experiments and gene expression profiles Parkinson, H.; Kapushesky, M.; Shojatalab, M. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl995	journal	January 2007
Refinement of Light-Responsive Transcript Lists Using Rice Oligonucleotide Arrays: Evaluation of Gene-Redundancy Jung, Ki-Hong; Dardick, Christopher; Bartley, Laura E. PLoS ONE, Vol. 3, Issue 10 https://doi.org/10.1371/journal.pone.0003337	journal	October 2008
Rice WRKY45 Plays a Crucial Role in Benzothiadiazole-Inducible Blast Resistance Shimono, Masaki; Sugano, Shoji; Nakayama, Akira The Plant Cell, Vol. 19, Issue 6 https://doi.org/10.1105/tpc.106.046250	journal	June 2007
PlaNet: Combined Sequence and Expression Comparisons across Plant Networks Derived from Seven Species Mutwil, Marek; Klie, Sebastian; Tohge, Takayuki The Plant Cell, Vol. 23, Issue 3 https://doi.org/10.1105/tpc.111.083667	journal	March 2011
Gramene Database: A Hub for Comparative Plant Genomics Jaiswal, Pankaj Methods in Molecular Biology https://doi.org/10.1007/978-1-60761-682-5_18	book	September 2010
OryzaExpress: An Integrated Database of Gene Expression Networks and Omics Annotations in Rice Hamada, Kazuki; Hongo, Kohei; Suwabe, Keita Plant and Cell Physiology, Vol. 52, Issue 2 https://doi.org/10.1093/pcp/pcq195	journal	December 2010
Auxin Biosynthesis Inhibitors, Identified by a Genomics-Based Approach, Provide Insights into Auxin Biosynthesis Soeno, Kazuo; Goda, Hideki; Ishii, Takahiro Plant and Cell Physiology, Vol. 51, Issue 4 https://doi.org/10.1093/pcp/pcq032	journal	April 2010
The map-based sequence of the rice genome Nature, Vol. 436, Issue 7052, p. 793-800 https://doi.org/10.1038/nature03895	journal	August 2005
Analysis of Alternatively Spliced Rice Transcripts Using Microarray Data Jung, Ki-Hong; Bartley, Laura E.; Cao, Peijian Rice, Vol. 2, Issue 1 https://doi.org/10.1007/s12284-008-9020-9	journal	December 2008
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
MArray: analysing single, replicated or reversed microarray experiments Wang, J.; Nygaard, V.; Smith-Sorensen, B. Bioinformatics, Vol. 18, Issue 8 https://doi.org/10.1093/bioinformatics/18.8.1139	journal	August 2002
Comparison of Transcript Profiling on Arabidopsis Microarray Platform Technologies Pylatuik, Jeffrey D.; Fobert, Pierre R. Plant Molecular Biology, Vol. 58, Issue 5 https://doi.org/10.1007/s11103-005-6506-3	journal	July 2005
Web Tools for Rice Transcriptome Analyses Jung, Ki-Hong; Jeon, Jong-Seong; An, Gynheung Journal of Plant Biology, Vol. 54, Issue 2 https://doi.org/10.1007/s12374-011-9146-y	journal	January 2011
Genome Relationships: The Grass Model in Current Research Devos, Katrien M.; Gale, Mike D. The Plant Cell, Vol. 12, Issue 5 https://doi.org/10.1105/tpc.12.5.637	journal	May 2000
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bolstad, B. M.; Irizarry, R. A.; Astrand, M. Bioinformatics, Vol. 19, Issue 2 https://doi.org/10.1093/bioinformatics/19.2.185	journal	January 2003
A dynamic gene expression atlas covering the entire life cycle of rice Wang, Lei; Xie, Weibo; Chen, Ying The Plant Journal, Vol. 61, Issue 5 https://doi.org/10.1111/j.1365-313X.2009.04100.x	journal	March 2010
Robust Locally Weighted Regression and Smoothing Scatterplots Cleveland, William S. Journal of the American Statistical Association, Vol. 74, Issue 368 https://doi.org/10.1080/01621459.1979.10481038	journal	December 1979
Detection of genomic deletions in rice using oligonucleotide microarrays Bruce, Myron; Hess, Ann; Bai, Jianfa BMC Genomics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2164-10-129	journal	January 2009
ATTED-II Updates: Condition-Specific Gene Coexpression to Extend Coexpression Analyses and Applications to a Broad Range of Flowering Plants Obayashi, T.; Nishida, K.; Kasahara, K. Plant and Cell Physiology, Vol. 52, Issue 2 https://doi.org/10.1093/pcp/pcq203	journal	January 2011
The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses: The Botany Array Resource Toufighi, Kiana; Brady, Siobhan M.; Austin, Ryan The Plant Journal, Vol. 43, Issue 1 https://doi.org/10.1111/j.1365-313X.2005.02437.x	journal	June 2005
CIBEX: Center for Information Biology gene EXpression database Ikeo, Kazuho; Ishi-i, Jun; Tamura, Takurou Comptes Rendus Biologies, Vol. 326, Issue 10-11 https://doi.org/10.1016/j.crvi.2003.09.034	journal	October 2003
The TIGR Rice Genome Annotation Resource: improvements and new features Ouyang, S.; Zhu, W.; Hamilton, J. Nucleic Acids Research, Vol. 35, Issue Database https://doi.org/10.1093/nar/gkl976	journal	January 2007
Rank of Correlation Coefficient as a Comparable Measure for Biological Significance of Gene Coexpression Obayashi, T.; Kinoshita, K. DNA Research, Vol. 16, Issue 5 https://doi.org/10.1093/dnares/dsp016	journal	September 2009
A new method for gene discovery in large-scale microarray data Yano, K. Nucleic Acids Research, Vol. 34, Issue 5 https://doi.org/10.1093/nar/gkl058	journal	March 2006
KEGG for representation and analysis of molecular networks involving diseases and drugs Kanehisa, Minoru; Goto, Susumu; Furumichi, Miho Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp896	journal	October 2009
RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions Sato, Y.; Antonio, B. A.; Namiki, N. Nucleic Acids Research, Vol. 39, Issue S1, p. D1141-D1148 https://doi.org/10.1093/nar/gkq1085	journal	November 2010
Towards a better bowl of rice: assigning function to tens of thousands of rice genes Jung, Ki-Hong; An, Gynheung; Ronald, Pamela C. Nature Reviews Genetics, Vol. 9, Issue 2 https://doi.org/10.1038/nrg2286	journal	February 2008
Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana Itoh, T.; Tanaka, T.; Barrero, R. A. Genome Research, Vol. 17, Issue 2 https://doi.org/10.1101/gr.5509507	journal	January 2007
Functional Annotation of the Arabidopsis Genome Using Controlled Vocabularies Berardini, Tanya Z.; Mundodi, Suparna; Reiser, Leonore Plant Physiology, Vol. 135, Issue 2 https://doi.org/10.1104/pp.104.040071	journal	June 2004
Cytoscape Web: an interactive web-based network browser Lopes, Christian T.; Franz, Max; Kazi, Farzana Bioinformatics, Vol. 26, Issue 18 https://doi.org/10.1093/bioinformatics/btq430	journal	July 2010
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies Jiao, Yuling; Lori Tausta, S.; Gandotra, Neeru Nature Genetics, Vol. 41, Issue 2 https://doi.org/10.1038/ng.282	journal	January 2009
Genome-Wide Analyses of Early Translational Responses to Elevated Temperature and High Salinity in Arabidopsis thaliana Matsuura, Hideyuki; Ishibashi, Yu; Shinmyo, Atsuhiko Plant and Cell Physiology, Vol. 51, Issue 3 https://doi.org/10.1093/pcp/pcq010	journal	January 2010
Global patterns of gene expression in rice cultivars undergoing a susceptible or resistant interaction with the parasitic plant Striga hermonthica Swarbrick, P. J.; Huang, K.; Liu, G. New Phytologist, Vol. 179, Issue 2 https://doi.org/10.1111/j.1469-8137.2008.02484.x	journal	July 2008
Genevestigator V3: A Reference Expression Database for the Meta-Analysis of Transcriptomes Hruz, Tomas; Laule, Oliver; Szabo, Gabor Advances in Bioinformatics, Vol. 2008 https://doi.org/10.1155/2008/420747	journal	January 2008
NCBI GEO: archive for high-throughput functional genomic data Barrett, T.; Troup, D. B.; Wilhite, S. E. Nucleic Acids Research, Vol. 37, Issue Database https://doi.org/10.1093/nar/gkn764	journal	January 2009
Collection, Mapping, and Annotation of Over 28,000 cDNA Clones from japonica Rice Kikuchi, S. Science, Vol. 301, Issue 5631 https://doi.org/10.1126/science.1081288	journal	July 2003
The Submergence Tolerance Regulator Sub1A Mediates Stress-Responsive Expression of AP2 / ERF Transcription Factors Jung, Ki-Hong; Seo, Young-Su; Walia, Harkamal Plant Physiology, Vol. 152, Issue 3 https://doi.org/10.1104/pp.109.152157	journal	January 2010
Bioconductor: open software development for computational biology and bioinformatics Gentleman, Robert C.; Carey, Vincent J.; Bates, Douglas M. Genome Biology, Vol. 5, Issue 10, p. R80 https://doi.org/10.1186/gb-2004-5-10-r80	journal	September 2004
arrayQualityMetrics—a bioconductor package for quality assessment of microarray data Kauffmann, Audrey; Gentleman, Robert; Huber, Wolfgang Bioinformatics, Vol. 25, Issue 3 https://doi.org/10.1093/bioinformatics/btn647	journal	December 2008
A gene expression map of Arabidopsis thaliana development Schmid, Markus; Davison, Timothy S.; Henz, Stefan R. Nature Genetics, Vol. 37, Issue 5 https://doi.org/10.1038/ng1543	journal	April 2005
RiceArrayNet: A Database for Correlating Gene Expression from Transcriptome Profiling, and Its Application to the Analysis of Coexpressed Genes in Rice Lee, Tae-Ho; Kim, Yeon-Ki; Pham, Thu Thi Minh Plant Physiology, Vol. 151, Issue 1 https://doi.org/10.1104/pp.109.139030	journal	July 2009
The Association of Multiple Interacting Genes with Specific Phenotypes in Rice Using Gene Coexpression Networks Ficklin, Stephen P.; Luo, Feng; Feltus, F. Alex Plant Physiology, Vol. 154, Issue 1 https://doi.org/10.1104/pp.110.159459	journal	July 2010
The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis Zhou, Ming; Coruh, Ceyda; Xu, Guanghui Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-021-27690-x	journal	January 2022
Dietary palmitic acid promotes a prometastatic memory via Schwann cells Pascual, Gloria; Domínguez, Diana; Elosúa-Bayes, Marc Nature, Vol. 599, Issue 7885 https://doi.org/10.1038/s41586-021-04075-0	journal	November 2021
The Rice Annotation Project Database (RAP-DB): 2008 update Project, Rice Annotation Nucleic Acids Research, Vol. 36, Issue Database, p. D1028-D1033 https://doi.org/10.1093/nar/gkm978	journal	January 2007
The Gene Ontology project in 2008. Consortium, Gene Ontology Oxford University Press (OUP) https://doi.org/10.17863/cam.52155	journalarticle	January 2008
Bioconductor : open software development for computational biology and bioinformatics C., Gentleman, Robert; J., Carey, Vincent; M., Bates, Douglas BioMed Central https://doi.org/10.21256/zhaw-1907	text	January 2004

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Comparative transcriptome profiling of a rice line carrying Xa39 and its parents triggered by Xanthomonas oryzae pv. oryzae provides novel insights into the broad-spectrum hypersensitive response Zhang, Fan; Huang, Li-Yu; Zhang, Fan BMC Genomics, Vol. 16, Issue 1 https://doi.org/10.1186/s12864-015-1329-3	journal	February 2015
Genome-wide comparison of Asian and African rice reveals high recent activity of DNA transposons Roffler, Stefan; Wicker, Thomas Mobile DNA, Vol. 6, Issue 1 https://doi.org/10.1186/s13100-015-0040-x	journal	April 2015
Differential Proteomic Analysis Using iTRAQ Reveals Alterations in Hull Development in Rice (Oryza sativa L.) Wang, Shuzhen; Chen, Wenyue; Xiao, Wenfei PLOS ONE, Vol. 10, Issue 7 https://doi.org/10.1371/journal.pone.0133696	journal	July 2015
Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition Deb, Arindam; Kundu, Sudip PLOS ONE, Vol. 10, Issue 9 https://doi.org/10.1371/journal.pone.0137295	journal	September 2015
Quantitative Trait Locus Mapping and Candidate Gene Analysis for Plant Architecture Traits Using Whole Genome Re-Sequencing in Rice Lim, Jung-Hyun; Yang, Hyun-Jung; Jung, Ki-Hong Molecules and Cells, Vol. 37, Issue 2 https://doi.org/10.14348/molcells.2014.2336	journal	February 2014
Mapping the microRNA Expression Profiles in Glyoxalase Overexpressing Salinity Tolerant Rice Tripathi, Anita; Chacon, Osmani; Singla-Pareek, Sneh Lata Current Genomics, Vol. 19, Issue 1 https://doi.org/10.2174/1389202918666170228134530	journal	December 2017
Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research Sharma, Rita; Cao, Peijian; Jung, Ki-Hong Frontiers in Plant Science, Vol. 4 https://doi.org/10.3389/fpls.2013.00330	journal	January 2013
Microarray Meta-Analysis Focused on the Response of Genes Involved in Redox Homeostasis to Diverse Abiotic Stresses in Rice de Abreu Neto, Joao B.; Frei, Michael Frontiers in Plant Science, Vol. 6 https://doi.org/10.3389/fpls.2015.01260	journal	January 2016
In silico Identification and Taxonomic Distribution of Plant Class C GH9 Endoglucanases Kundu, Siddhartha; Sharma, Rita Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.01185	journal	August 2016
A Systematic View of the MLO Family in Rice Suggests Their Novel Roles in Morphological Development, Diurnal Responses, the Light-Signaling Pathway, and Various Stress Responses Nguyen, Van N. T.; Vo, Kieu T. X.; Park, Hyon Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.01413	journal	September 2016
Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage Kumar, Manu; Gho, Yun-Shil; Jung, Ki-Hong Frontiers in Plant Science, Vol. 8 https://doi.org/10.3389/fpls.2017.01120	journal	June 2017
ARMOUR – A Rice miRNA: mRNA Interaction Resource Sanan-Mishra, Neeti; Tripathi, Anita; Goswami, Kavita Frontiers in Plant Science, Vol. 9 https://doi.org/10.3389/fpls.2018.00602	journal	May 2018
Genome-Wide Computational Identification of Biologically Significant Cis-Regulatory Elements and Associated Transcription Factors from Rice Plants, Vol. 8, Issue 11 https://doi.org/10.3390/plants8110441	journal	October 2019

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Title: The Rice Oligonucleotide Array Database: an atlas of rice gene expression

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