Guenin S, Mauriat M, Pelloux J, Van Wuytswinkel O, Bellini C, Gutierrez L: Normalization of qRT-PCR data: the necessity of adopting a systematic, experimental conditions-specific, validation of references. J Exp Bot. 2009, 60 (2): 487-493. 10.1093/jxb/ern305.
Article
PubMed
CAS
Google Scholar
Gutierrez L, Mauriat M, Guenin S, Pelloux J, Lefebvre JF, Louvet R, Rusterucci C, Moritz T, Guerineau F, Bellini C, Van Wuytswinkel O: The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction (RT-PCR) analysis in plants. Plant Biotechnol J. 2008, 6 (6): 609-618. 10.1111/j.1467-7652.2008.00346.x.
Article
PubMed
CAS
Google Scholar
Nettleton D: A discussion of statistical methods for design and analysis of microarray experiments for plant scientists. Plant Cell. 2006, 18 (9): 2112-2121. 10.1105/tpc.106.041616.
Article
PubMed
CAS
PubMed Central
Google Scholar
Quackenbush J: Microarray data normalization and transformation. Nat Genet. 2002, 32 (Suppl): 496-501. 10.1038/ng1032.
Article
PubMed
CAS
Google Scholar
Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W: GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol. 2004, 136 (1): 2621-2632. 10.1104/pp.104.046367.
Article
PubMed
CAS
PubMed Central
Google Scholar
Toufighi K, Brady SM, Austin R, Ly E, Provart NJ: The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses. Plant J. 2005, 43 (1): 153-163. 10.1111/j.1365-313X.2005.02437.x.
Article
PubMed
CAS
Google Scholar
Caldana C, Scheible WR, Mueller-Roeber B, Ruzicic S: A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors. Plant Methods. 2007, 3: 7. 10.1186/1746-4811-3-7.
Article
PubMed
PubMed Central
Google Scholar
Czechowski T, Bari RP, Stitt M, Scheible WR, Udvardi MK: Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. Plant J. 2004, 38 (2): 366-379. 10.1111/j.1365-313X.2004.02051.x.
Article
PubMed
CAS
Google Scholar
Kakar K, Wandrey M, Czechowski T, Gaertner T, Scheible WR, Stitt M, Torres-Jerez I, Xiao Y, Redman JC, Wu HC, Cheung F, Town CD, Udvardi MK: A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula. Plant Methods. 2008, 4: 18. 10.1186/1746-4811-4-18.
Article
PubMed
PubMed Central
Google Scholar
Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible WR: Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol. 2005, 139 (1): 5-17. 10.1104/pp.105.063743.
Article
PubMed
CAS
PubMed Central
Google Scholar
Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP: Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlations. Biotechnol Lett. 2004, 26 (6): 509-515. 10.1023/B:BILE.0000019559.84305.47.
Article
PubMed
CAS
Google Scholar
Andersen CL, Jensen JL, Orntoft TF: Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 2004, 64 (15): 5245-5250. 10.1158/0008-5472.CAN-04-0496.
Article
PubMed
CAS
Google Scholar
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002, 3 (7): RESEARCH0034. 10.1186/gb-2002-3-7-research0034.
Article
PubMed
PubMed Central
Google Scholar
Barsalobres-Cavallari CF, Severino FE, Maluf MP, Maia IG: Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions. BMC Mol Biol. 2009, 10: 1. 10.1186/1471-2199-10-1.
Article
PubMed
PubMed Central
Google Scholar
Exposito-Rodriguez M, Borges AA, Borges-Perez A, Perez JA: Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. BMC Plant Biol. 2008, 8: 131. 10.1186/1471-2229-8-131.
Article
PubMed
PubMed Central
Google Scholar
Hu R, Fan C, Li H, Zhang Q, Fu YF: Evaluation of putative reference genes for gene expression normalization in soybean by quantitative real-time RT-PCR. BMC Mol Biol. 2009, 10: 93. 10.1186/1471-2199-10-93.
Article
PubMed
PubMed Central
Google Scholar
Reid KE, Olsson N, Schlosser J, Oenq F, Lund ST: An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development. BMC Plant Biol. 2006, 6: 27-37. 10.1186/1471-2229-6-27.
Article
PubMed
PubMed Central
Google Scholar
Flavell R: Role of model plant species. Methods Mol Biol. 2009, 513: 1-18. full_text.
Article
PubMed
CAS
Google Scholar
Fitzgerald MA, McCouch SR, Hall RD: Not just a grain of rice: the quest for quality. Trends Plant Sci. 2009, 14 (3): 133-139. 10.1016/j.tplants.2008.12.004.
Article
PubMed
CAS
Google Scholar
Jain M, Nijhawan A, Tyagi AK, Khurana JP: Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem Biophys Res Commun. 2006, 345 (2): 646-651. 10.1016/j.bbrc.2006.04.140.
Article
PubMed
CAS
Google Scholar
Narsai R, Howell KA, Carroll A, Ivanova A, Millar AH, Whelan J: Defining core metabolic and transcriptomic responses to oxygen availability in rice embryos and young seedlings. Plant Physiol. 2009, 151 (1): 306-322. 10.1104/pp.109.142026.
Article
PubMed
CAS
PubMed Central
Google Scholar
Jiao Y, Tausta SL, Gandotra N, Sun N, Liu T, Clay NK, Ceserani T, Chen M, Ma L, Holford M, Zhang HY, Zhao H, Deng XW, Nelson T: A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies. Nat Genet. 2009, 41 (2): 258-263. 10.1038/ng.282.
Article
PubMed
CAS
Google Scholar
Remm M, Storm CE, Sonnhammer EL: Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol. 2001, 314 (5): 1041-1052. 10.1006/jmbi.2000.5197.
Article
PubMed
CAS
Google Scholar
Mosquera G, Giraldo MC, Khang CH, Coughlan S, Valent B: Interaction transcriptome analysis identifies Magnaporthe oryzae BAS1-4 as Biotrophy-associated secreted proteins in rice blast disease. Plant Cell. 2009, 21 (4): 1273-1290. 10.1105/tpc.107.055228.
Article
PubMed
CAS
PubMed Central
Google Scholar
Van Aken O, Zhang B, Carrie C, Uggalla V, Paynter E, Giraud E, Whelan J: Defining the Mitochondrial Stress Response in Arabidopsis thaliana. Mol Plant. 2009, 2 (6): 1310-1324. 10.1093/mp/ssp053.
Article
PubMed
CAS
Google Scholar
Canales RD, Luo Y, Willey JC, Austermiller B, Barbacioru CC, Boysen C, Hunkapiller K, Jensen RV, Knight CR, Lee KY, Ma Y, Maqsodi B, Papallo A, Peters EH, Poulter K, Ruppel PL, Samaha RR, Shi L, Yang W, Zhang L, Goodsaid FM: Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol. 2006, 24 (9): 1115-1122. 10.1038/nbt1236.
Article
PubMed
CAS
Google Scholar
Howell KA, Narsai R, Carroll A, Ivanova A, Lohse M, Usadel B, Millar AH, Whelan J: Mapping metabolic and transcript temporal switches during germination in rice highlights specific transcription factors and the role of RNA instability in the germination process. Plant Physiol. 2009, 149 (2): 961-980. 10.1104/pp.108.129874.
Article
PubMed
CAS
PubMed Central
Google Scholar
Lasanthi-Kudahettige R, Magneschi L, Loreti E, Gonzali S, Licausi F, Novi G, Beretta O, Vitulli F, Alpi A, Perata P: Transcript profiling of the anoxic rice coleoptile. Plant Physiol. 2007, 144 (1): 218-231. 10.1104/pp.106.093997.
Article
PubMed
CAS
PubMed Central
Google Scholar
Xue LJ, Zhang JJ, Xue HW: Characterization and expression profiles of miRNAs in rice seeds. Nucleic Acids Res. 2009, 37 (3): 916-930. 10.1093/nar/gkn998.
Article
PubMed
CAS
PubMed Central
Google Scholar
Li M, Xu W, Yang W, Kong Z, Xue Y: Genome-wide gene expression profiling reveals conserved and novel molecular functions of the stigma in rice. Plant Physiol. 2007, 144 (4): 1797-1812. 10.1104/pp.107.101600.
Article
PubMed
CAS
PubMed Central
Google Scholar
Jain M, Nijhawan A, Arora R, Agarwal P, Ray S, Sharma P, Kapoor S, Tyagi AK, Khurana JP: 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. 2007, 143 (4): 1467-1483. 10.1104/pp.106.091900.
Article
PubMed
CAS
PubMed Central
Google Scholar
Hu W, Hu G, Han B: Genome-wide survey and expression profiling of heat shock proteins and heat shock factors revealed overlapped and stress specific response under abiotic stresses in rice. Plant Science. 2009, 176: 583-590. 10.1016/j.plantsci.2009.01.016.
Article
PubMed
CAS
Google Scholar
Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J, Xu J, Cui X, Close TJ: Comparative transcriptional profiling of two contrasting rice genotypes under salinity stress during the vegetative growth stage. Plant Physiol. 2005, 139 (2): 822-835. 10.1104/pp.105.065961.
Article
PubMed
CAS
PubMed Central
Google Scholar
Walia H, Wilson C, Zeng L, Ismail AM, Condamine P, Close TJ: Genome-wide transcriptional analysis of salinity stressed japonica and indica rice genotypes during panicle initiation stage. Plant Mol Biol. 2007, 63 (5): 609-623. 10.1007/s11103-006-9112-0.
Article
PubMed
CAS
PubMed Central
Google Scholar
Zheng L, Huang F, Narsai R, Wu J, Giraud E, He F, Cheng L, Wang F, Wu P, Whelan J, Shou H: Physiological and transcriptome analysis of iron and phosphorus interaction in rice seedlings. Plant Physiol. 2009, 151 (1): 262-74. 10.1104/pp.109.141051.
Article
PubMed
CAS
PubMed Central
Google Scholar
Norton GJ, Lou-Hing DE, Meharg AA, Price AH: Rice-arsenate interactions in hydroponics: whole genome transcriptional analysis. J Exp Bot. 2008, 59 (8): 2267-2276. 10.1093/jxb/ern097.
Article
PubMed
CAS
PubMed Central
Google Scholar
Swarbrick PJ, Huang K, Liu G, Slate J, Press MC, Scholes JD: Global patterns of gene expression in rice cultivars undergoing a susceptible or resistant interaction with the parasitic plant Striga hermonthica. New Phytol. 2008, 179 (2): 515-529. 10.1111/j.1469-8137.2008.02484.x.
Article
PubMed
CAS
Google Scholar
Ribot C, Hirsch J, Balzergue S, Tharreau D, Notteghem JL, Lebrun MH, Morel JB: Susceptibility of rice to the blast fungus, Magnaporthe grisea. J Plant Physiol. 2008, 165 (1): 114-124. 10.1016/j.jplph.2007.06.013.
Article
PubMed
CAS
Google Scholar
Hirose N, Makita N, Kojima M, Kamada-Nobusada T, Sakakibara H: Overexpression of a type-A response regulator alters rice morphology and cytokinin metabolism. Plant Cell Physiol. 2007, 48 (3): 523-539. 10.1093/pcp/pcm022.
Article
PubMed
CAS
Google Scholar
Jain M, Khurana JP: Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. Febs J. 2009, 276 (11): 3148-3162. 10.1111/j.1742-4658.2009.07033.x.
Article
PubMed
CAS
Google Scholar