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How to cite PLEXdb

Publications about PLEXdb

To Cite PLEXdb
Dash S, Van Hemert J, Hong L, Wise RP, Dickerson JA. 2012.
PLEXdb: gene expression resources for plants and plant pathogens.
Nucleic Acids Research 40 (D1): D1194-D1201.
Go to the NAR article

**Please use the above if you want to cite PLEXdb or your publication uses tools or data from PLEXdb.

Past Publications

Publications which cite or use PLEXdb/BarleyBase
(Also includes publications that support data in PLEXdb)

Thermotolerance Responses in Ripening Berries of Vitis vinifera L. cv Muscat Hamburg .
Pablo Carbonell-Bejerano, Eva Santa Maria, Rafael Torres-Perez, Carolina Royo, Diego Lijavetzky, Gema Bravo, Jone Aguirreolea, Manuel Sanchez-Diaz, M. Carmen Antolin, and Jose M. Martinez-Zapater
Plant Cell Physiol first published online May 9, 2013 doi:10.1093/pcp/pct071.
PubMed: 23659918
PLEXdb: browse VV46 experiment data

EBR1 genomic expansion and its role in virulence of Fusarium species.

Cbf genes of the Fr-A2 allele are differentially regulated between long-term cold acclimated crown tissue of freeze-resistant and - susceptible, winter wheat mutant lines..
Sutton F, Chen DG, Ge X, Kenefick D.
BMC Plant Biol. 2009 Mar 23;9:34. doi: 10.1186/1471-2229-9-34.
PubMed: 19309505
PLEXdb: browse TA22 experiment data

Transcript and metabolite analysis in Trincadeira cultivar reveals novel information regarding the dynamics of grape ripening..
Fortes AM, Agudelo-Romero P, Silva MS, Ali K, Sousa L, Maltese F, Choi YH, Grimplet J, Martinez-Zapater JM, Verpoorte R, Pais MS.
BMC Plant Biol 2011 Nov 2;11:149.
PubMed: 22047180
PLEXdb: browse VV45 experiment data

Berry skin development in Norton grape: distinct patterns of transcriptional regulation and flavonoid biosynthesis..
Ali MB, Howard S, Chen S, Wang Y, Yu O, Kovacs LG, Qiu W.
BMC Plant Biol 2011 Jan 10;11:7.
PubMed: 21219654
PLEXdb: browse VV42 experiment data

Understanding the molecular events underpinning cultivar differences in physiological performance and heat tolerance.
Nicola S. Cottee, Iain W. Wilson, Daniel K.Y. Tan, Michael P. Bange
PLEXdb: browse GO12 experiment data

Diverse correlation patterns between microRNAs and their targets during tomato fruit development indicates different modes of microRNA actions..
Lopez-Gomollon S, Mohorianu I, Szittya G, Moulton V, Dalmay T.
Planta 2012 Aug 26.
PubMed: 22922939
PLEXdb: browse LE21 experiment data

Poplar extrafloral nectaries: two types, two strategies of indirect defenses against herbivores..
Escalante-Pérez M, Jaborsky M, Lautner S, Fromm J, Müller T, Dittrich M, Kunert M, Boland W, Hedrich R, Ache P.
Plant Physiol 2012 Jul;159(3):1176-91.
PubMed: 22573802
PLEXdb: browse PT49 experiment data

Transcriptomic analysis of grape (Vitis vinifera L.) leaves during and after recovery from heat stress.
Wang L, Li S, Wang J, Cramer G, Dai Z, Duan W, Xu H, Wu B, Fan P.
BMC Plant Biol. 2012 Sep 28;12(1):174.
PubMed: 23016701
PLEXdb: browse VV40 experiment data

Experimental sink removal induces stress responses, including shifts in amino acid and phenylpropanoid metabolism, in soybean leaves..
Turner GW, Cuthbertson DJ, Voo SS, Settles ML, Grimes HD, Lange BM.
Planta 2012 May;235(5):939-54
PubMed: 22109846
PLEXdb: browse GM50 experiment data

Transcriptome analysis of nitrogen-efficient rice over-expressing alanine aminotransferase..
Beatty PH, Shrawat AK, Carroll RT, Zhu T, Good AG.
Plant Biotechnol J 2009 Aug;7(6):562-76.
PubMed: 19508275
PLEXdb: browse OS98 experiment data

Molecular features of secondary vascular tissue regeneration after bark girdling in Populus..
Zhang J, Gao G, Chen JJ, Taylor G, Cui KM, He XQ.
New Phytol 2011 Dec;192(4):869-84.
PubMed: 21883236
PLEXdb: browse PT46 experiment data

Genome-wide transcriptomic analysis of cotton under drought stress reveal significant down-regulation of genes and pathways involved in fibre elongation and up-regulation of defense responsive genes..
Padmalatha KV, Dhandapani G, Kanakachari M, Kumar S, Dass A, Patil DP, Rajamani V, Kumar K, Pathak R, Rawat B, Leelavathi S, Reddy PS, Jain N, Powar KN, Hiremath V, Katageri IS, Reddy MK, Solanke AU, Reddy VS, Kumar PA.
Plant Mol Biol 2012 Feb;78(3):223-46.
PubMed: 22143977
PLEXdb: browse GO7 experiment data
browse GO8 experiment data
browse GO9 experiment data

OsMYB2P-1, an R2R3 MYB transcription factor, is involved in the regulation of phosphate-starvation responses and root architecture in rice..
Dai X, Wang Y, Yang A, Zhang WH.
Plant Physiol 2012 May;159(1):169-83.
PubMed: 22395576
PLEXdb: browse OS96 experiment data

Berry Flesh and Skin Ripening Features in Vitis vinifera as Assessed by Transcriptional Profiling.
Diego Lijavetzky, Pablo Carbonell-Bejerano1,Jerome Grimplet, Gema Bravo, Pilar Flores, Jose Fenoll, Pilar Hellin, Juan Carlos Oliveros, Jose M. Martinez-Zapater.
PLoS ONE 7(6): e39547. doi:10.1371/journal.pone.0039547(2012).
PubMed: 22768087
PLEXdb: browse VV33 experiment data

Transcriptional and metabolic analysis of senescence induced by preventing pollination in maize.
Sekhon RS, Childs K, Santoro N, Foster C, Buell CR, de Leon N, Kaeppler SM
Plant Physiology
PubMed: 22732243
PLEXdb: browse ZM54 experiment data

Low red/far-red ratios reduce Arabidopsis resistance to Botrytis cinerea and jasmonate responses via a COI1-JAZ10-dependent, salicylic acid-independent mechanism..
Cerrudo I, Keller MM, Cargnel MD, Demkura PV, de Wit M, Patitucci MS, Pierik R, Pieterse CM, Ballaré CL.
Plant Physiol 2012 Apr;158(4):2042-52.
PubMed: 22371506
PLEXdb: browse AT139 experiment data

Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches..
Fukushima A, Nishizawa T, Hayakumo M, Hikosaka S, Saito K, Goto E, Kusano M.
Plant Physiol 2012 Apr;158(4):1487-502.
PubMed: 22307966
PLEXdb: browse LE20 experiment data

Inhibition of Glutamine Synthetase by Phosphinothricin Leads to Transcriptome Reprograming in Root Nodules of Medicago truncatula..
Seabra AR, Pereira PA, Becker JD, Carvalho HG.
Mol Plant Microbe Interact 2012 Jul;25(7):976-92.
PubMed: 22414438
PLEXdb: browse ME25 experiment data

Transcriptional responses towards diffusible signals from symbiotic microbes reveal MtNFP- and MtDMI3-dependent reprogramming of host gene expression by AM fungal LCOs..
Czaja LF, Hogekamp C, Lamm P, Maillet F, Andres Martinez E, Samain E, Dénarié J, Küster H, Hohnjec N.
Plant Physiol 2012 May 31.
PubMed: 22652128
PLEXdb: browse ME22 experiment data
browse ME23 experiment data
browse ME24 experiment data

Transcriptome variation along bud development in grapevine (Vitis vinifera L.).
Diaz-Riquelme, J., Grimplet, J., Martinez-Zapater, J. M., & Carmona, M. J.
BMC Plant Biology 12, no. 1 (2012): 181.
PubMed: 23035802
PLEXdb: browse VV36 experiment data

Genomic associations for drought tolerance on the short arm of wheat chromosome 4B..
Kadam S, Singh K, Shukla S, Goel S, Vikram P, Pawar V, Gaikwad K, Khanna-Chopra R, Singh N.
Funct Integr Genomics 2012 Apr 5.
PubMed: 22476619
PLEXdb: browse TA44 experiment data

Transcriptome-based examination of putative pollen allergens of rice (Oryza sativa ssp. japonica)..
Russell SD, Bhalla PL, Singh MB.
Mol Plant 2008 Sep;1(5):751-9.
PubMed: 19825578
PLEXdb: browse OS94 experiment data

The Lectin Receptor Kinase-VI.2 Is Required for Priming and Positively Regulates Arabidopsis Pattern-Triggered Immunity..
Singh P, Kuo YC, Mishra S, Tsai CH, Chien CC, Chen CW, Desclos-Theveniau M, Chu PW, Schulze B, Chinchilla D, Boller T, Zimmerli L.
Plant Cell 2012 Mar;24(3):1256-70.
PubMed: 22427336
PLEXdb: browse AT136 experiment data

Plant Genes Related to Gibberellin Biosynthesis and Signaling Are Differentially Regulated during the Early Stages of AM Fungal Interactions..
Ortu G, Balestrini R, Pereira PA, Becker JD, Küster H, Bonfante P.
Mol Plant 2012 Mar 26.
PubMed: 22451647
PLEXdb: browse ME20 experiment data

MicroRNA profiles and their control of male gametophyte development in rice..
Peng H, Chun J, Ai TB, Tong YA, Zhang R, Zhao MM, Chen F, Wang SH.
Plant Mol Biol 2012 Mar 9.
PubMed: 22403030
PLEXdb: browse OS93 experiment data

OsWRKY22, a monocot WRKY gene, plays a role in the resistance response to blast..
Abbruscato P, Nepusz T, Mizzi L, Del Corvo M, Morandini P, Fumasoni I, Michel C, Paccanaro A, Guiderdoni E, Schaffrath U, Morel JB, Piffanelli P, Faivre-Rampant O.
Mol Plant Pathol 2012 Mar 23.
PubMed: 22443363
PLEXdb: browse OS91 experiment data

Reasons for lower transformation efficiency in indica rice using Agrobacterium tumefaciens-mediated transformation: lessons from transformation assays and genome-wide expression profiling..
Tie W, Zhou F, Wang L, Xie W, Chen H, Li X, Lin Y.
Plant Mol Biol 2012 Jan;78(1-2):1-18.
PubMed: 22089972
PLEXdb: browse OS87 experiment data

Global analysis of expression profiles of rice receptor-like kinase genes..
Gao LL, Xue HW.
Mol Plant 2012 Jan;5(1):143-53.
PubMed: 21765177
PLEXdb: browse OS89 experiment data

Transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes provides insight into LeMADS-RIN-regulated ethylene-dependent as well as ethylene-independent aspects of ripening in tomato..
Kumar R, Sharma MK, Kapoor S, Tyagi AK, Sharma AK.
Mol Genet Genomics 2012 Mar;287(3):189-203.
PubMed: 22212279
PLEXdb: browse LE19 experiment data

Comparative transcriptome analysis of stylar canal cells identifies novel candidate genes implicated in the self-incompatibility response of Citrus clementina..
Caruso M, Merelo P, Distefano G, La Malfa S, Lo Piero AR, Tadeo FR, Talon M, Gentile A.
BMC Plant Biol 2012 Feb 14;12:20.
PubMed: 22333138
PLEXdb: browse CT8 experiment data

Volatiles of two growth-inhibiting rhizobacteria commonly engage AtWRKY18 function..
Wenke K, Wanke D, Kilian J, Berendzen K, Harter K, Piechulla B.
Plant J 2011 Dec 21.
PubMed: 22188129
PLEXdb: browse AT134 experiment data

An association transcriptomics approach to the prediction of hybrid performance.
Stokes D., Fraser F., Morgan C., O'Neill C. M., Dreos R., Magusin A., Szalma S., Bancroft I.
Molecular Breeding 26 (1) 91-106 DOI:10.1007/s11032-009-9379-3
PLEXdb: browse ZM51 experiment data

Comparison of four ChIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data..
Malone BM, Tan F, Bridges SM, Peng Z.
PLoS One 2011;6(9):e25260.
PubMed: 21984925
PLEXdb: browse OS80 experiment data

The single functional blast resistance gene Pi54 activates a complex defence mechanism in rice..
Gupta SK, Rai AK, Kanwar SS, Chand D, Singh NK, Sharma TR.
J Exp Bot 2012 Jan;63(2):757-72.
PubMed: 22058403
PLEXdb: browse OS79 experiment data

Kerchev PI, Pellny TK, Vivancos PD, Kiddle G, Hedden P, Driscoll S, Vanacker H, Verrier P, Hancock RD, Foyer CH..
The transcription factor ABI4 Is required for the ascorbic acid-dependent regulation of growth and regulation of jasmonate-dependent defense signaling pathways in Arabidopsis.
Plant Cell 2011 Sep;23(9):3319-34.
PubMed: 21926335
PLEXdb: browse AT130 experiment data
browse AT131 experiment data
browse AT132 experiment data

LEAFY target genes reveal floral regulatory logic, cis motifs, and a link to biotic stimulus response..
Winter CM, Austin RS, Blanvillain-Baufumé S, Reback MA, Monniaux M, Wu MF, Sang Y, Yamaguchi A, Yamaguchi N, Parker JE, Parcy F, Jensen ST, Li H, Wagner D.
Dev Cell 2011 Apr 19;20(4):430-43.
PubMed: 21497757
PLEXdb: browse AT125 experiment data

Biotin Deficiency Causes Spontaneous Cell Death and Activation of Defense Signaling..
Li J, Brader G, Helenius E, Kariola T, Palva ET.
Plant J 2011 Nov 29.
PubMed: 22126457
PLEXdb: browse AT127 experiment data

In planta stage-specific fungal gene profiling elucidates the molecular strategies of Fusarium graminearum growing inside wheat coleoptiles.
Xiao-Wei Zhang, Lei-Jie Jia, Yan Zhang, Gang Jiang, Xuan Li, Dong Zhang, Wei-Hua Tang
Plant Cell (2012) 24(12).
PubMed: 23266949
PLEXdb: browse FG19 experiment data

Translatome and metabolome effects triggered by gibberellins during rosette growth in Arabidopsis..
Ribeiro DM, Araújo WL, Fernie AR, Schippers JH, Mueller-Roeber B.
J Exp Bot 2012 Jan 30.
PubMed: 22291129
PLEXdb: browse AT124 experiment data

Early transcriptional defense responses in Arabidopsis cell suspension culture under high-light conditions..
González-Pérez S, Gutiérrez J, García-García F, Osuna D, Dopazo J, Lorenzo Ó, Revuelta JL, Arellano JB.
Plant Physiol 2011 Jul;156(3):1439-56.
PubMed: 21531897
PLEXdb: browse AT123 experiment data

Glycerol-3-phosphate is a critical mobile inducer of systemic immunity in plants..
Chanda B, Xia Y, Mandal MK, Yu K, Sekine KT, Gao QM, Selote D, Hu Y, Stromberg A, Navarre D, Kachroo A, Kachroo P.
Nat Genet 2011 May;43(5):421-7.
PubMed: 21441932
PLEXdb: browse AT122 experiment data

Evidence that XRN4, an Arabidopsis homolog of exoribonuclease XRN1, preferentially impacts transcripts with certain sequences or in particular functional categories..
Rymarquis LA, Souret FF, Green PJ.
RNA 2011 Mar;17(3):501-11.
PubMed: 21224377
PLEXdb: browse AT120 experiment data

Negative regulation of defence signalling pathways by the EDR1 protein kinase..
Christiansen KM, Gu Y, Rodibaugh N, Innes RW.
Mol Plant Pathol 2011 Oct;12(8):746-58.
PubMed: 21726375
PLEXdb: browse AT119 experiment data

Metabolome and transcriptome of the interaction between Ustilago maydis and Fusarium verticillioides in vitro.
Jonkers, W., Rodriguez Estrada, A.E., Lee, K., Breakspear, A., May, G. and Kistler, H.C.
Applied and Environmental Microbiology 78(10): 3656-3667.
PubMed: 22407693
PLEXdb: browse NF3 experiment data
browse NF4 experiment data

Timing of plant immune responses by a central circadian regulator..
Wang W, Barnaby JY, Tada Y, Li H, Tör M, Caldelari D, Lee DU, Fu XD, Dong X.
Nature 2011 Feb 3;470(7332):110-4.
PubMed: 21293378
PLEXdb: browse AT118 experiment data

Arabidopsis BRCA2 and RAD51 proteins are specifically involved in defense gene transcription during plant immune responses..
Wang S, Durrant WE, Song J, Spivey NW, Dong X.
Proc Natl Acad Sci U S A 2010 Dec 28;107(52):22716-21.
PubMed: 21149701
PLEXdb: browse AT117 experiment data

Broad-spectrum acquired resistance in barley induced by the Pseudomonas pathosystem shares transcriptional components with Arabidopsis SAR. .
Colebrook EH, Creissen G, McGrann GRD, Dreos R, Lamb C and Boyd LA
Molecular Plant-Microbe Interactions 25, No. 5, pp. 658-667 (2012).
PubMed: 22250583
PLEXdb: browse BB92 experiment data

Neonicotinoid insecticides induce salicylate-associated plant defense responses..
Ford KA, Casida JE, Chandran D, Gulevich AG, Okrent RA, Durkin KA, Sarpong R, Bunnelle EM, Wildermuth MC.
Proc Natl Acad Sci U S A 2010 Oct 12;107(41):17527-32.
PubMed: 20876120
PLEXdb: browse AT110 experiment data

The Wor1-like protein Fgp1 regulates pathogenicity, toxin synthesis and reproduction in the phytopathogenic fungus Fusarium graminearum.
Jonkers, W., Dong, Y., Broz, K., and Kistler, H.C.
PLoS Pathogens 8(5): e1002724.[2012].
PubMed: 22693448
PLEXdb: browse FG18 experiment data
browse NF1 experiment data
browse NF6 experiment data
browse NF7 experiment data

MutS HOMOLOG1 is a nucleoid protein that alters mitochondrial and plastid properties and plant response to high light..
Xu YZ, Arrieta-Montiel MP, Virdi KS, de Paula WB, Widhalm JR, Basset GJ, Davila JI, Elthon TE, Elowsky CG, Sato SJ, Clemente TE, Mackenzie SA.
Plant Cell 2011 Sep;23(9):3428-41.
PubMed: 21934144
PLEXdb: browse GM46 experiment data

Strigolactone Biosynthesis in Medicago truncatula and Rice Requires the Symbiotic GRAS-Type Transcription Factors NSP1 and NSP2..
Liu W, Kohlen W, Lillo A, Op den Camp R, Ivanov S, Hartog M, Limpens E, Jamil M, Smaczniak C, Kaufmann K, Yang WC, Hooiveld GJ, Charnikhova T, Bouwmeester HJ, Bisseling T, Geurts R.
Plant Cell 2011 Oct;23(10):3853-65.
PubMed: 22039214
PLEXdb: browse ME19 experiment data

High and low acid lemons: origin and transcriptome comparisons.
Aprile, A., Federici, C. T., Close, T.. Roose, M. L., De Bellis, L and Cattivelli L.
Acta Horticulturae 892:37-42(2011).
PLEXdb: browse CT1 experiment data

Expression of the H+-ATPase AHA10 proton pump is associated with citric acid accumulation in lemon juice sac cells.
Aprile, A., Federici, C., Close, T. J., De Bellis, L. and Cattivelli L and Roose, M. L.
Funct. Integr. Genomics 11:551-563 (2011)..
PubMed: 21556928
PLEXdb: browse CT1 experiment data

Quantitative and Temporal Definition of the Mla Transcriptional Regulon During Barley-Powdery Mildew Interactions.
Matthew J. Moscou, Nick Lauter, Rico A. Caldo, Dan Nettleton, and Roger P. Wise
Molecular Plant-Microbe Interactions 2011 24:6, 694-705 .
PLEXdb: browse BB2 experiment data
browse BB10 experiment data

Cytokinin-mediated source/sink modifications improve drought tolerance and increase grain yield in rice under water-stress..
Peleg Z, Reguera M, Tumimbang E, Walia H, Blumwald E.
Plant Biotechnol J 2011 Sep;9(7):747-58.
PubMed: 21284800
PLEXdb: browse OS72 experiment data

Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.)..
Laudencia-Chingcuanco D, Ganeshan S, You F, Fowler B, Chibbar R, Anderson O.
BMC Genomics 2011 Jun 7;12:299.
PubMed: 21649926
PLEXdb: browse TA42 experiment data

Laser-microdissection unravels cell-type specific transcription in arbuscular mycorrhizal roots, including CAAT-box TF gene expression correlating with fungal contact and spread..
Hogekamp C, Arndt D, Pereira P, Becker JD, Hohnjec N, Küster H.
Plant Physiol 2011 Oct 27.
PubMed: 22034628
PLEXdb: browse ME18 experiment data

PLEXdb: gene expression resources for plants and plant pathogens.
Sudhansu Dash, John Van Hemert, Lu Hong, Roger P. Wise and Julie A. Dickerson.
Nucleic Acids Research 40 (D1): D1194-D1201.
PubMed: 22084198

Inducible maize defense mechanisms against the corn borer Sesamia nonagrioides: a transcriptome and biochemical approach..
Rodríguez VM, Santiago R, Malvar RA, Butrón A.
Mol Plant Microbe Interact 2011 Sep 14.
PubMed: 21916555
PLEXdb: browse ZM48 experiment data

Plant preconditioning with different aphid genotypes alters aphid growth rate and plant gene expression.
Sharon E. Zytynska, Violaine Jourdie, Richard F. Preziosi
in submission
PLEXdb: browse BB107 experiment data

Genome-wide transcriptome and proteome analyses of tobacco psaA and psbA deletion mutants..
Leelavathi S, Bhardwaj A, Kumar S, Dass A, Pathak R, Pandey SS, Tripathy BC, Padmalatha KV, Dhandapani G, Kanakachari M, Solanke AU, Kumar PA, Cella R, Siva Reddy V.
Plant Mol Biol 2011 Jul;76(3-5):407-23.
PubMed: 21327516
PLEXdb: browse LE17 experiment data

Combined analysis of transcriptome and metabolite data reveals extensive differences between black and brown nearly-isogenic soybean (Glycine max) seed coats enabling the identification of pigment isogenes..
Kovinich N, Saleem A, Arnason JT, Miki B.
BMC Genomics 2011 Jul 29;12:381.
PubMed: 21801362
PLEXdb: browse GM43 experiment data

Six nonnodulating plant mutants defective for Nod factor-induced transcriptional changes associated with the legume-rhizobia symbiosis..
Mitra RM, Shaw SL, Long SR.
Proc Natl Acad Sci U S A 2004 Jul 6;101(27):10217-22.
PubMed: 15220482
PLEXdb: browse ME15 experiment data

Complex regulation of symbiotic functions is coordinated by MucR and quorum sensing in Sinorhizobium meliloti..
Mueller K, González JE.
J Bacteriol 2011 Jan;193(2):485-96.
PubMed: 21057009
PLEXdb: browse ME14 experiment data

Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing..
Mingming Xin, Yu Wang, Yingyin Yao, Na Song, Zhaorong Hu, Dandan Qin, Chaojie Xie, Huiru Peng, Zhongfu Ni,and Qixin Sun.
BMC Plant Biol 2011 Apr 7;11:61.
PubMed: 21473757
PLEXdb: browse TA39 experiment data

The transcriptome of Fusarium graminearum during the infection of wheat.
Lyse, Erik, Seong, K.Y, and H. Corby Kistler
Mol Plant Microbe Interact.(2011) 24(9):995-1000 (DOI: 10.1094/MPMI-02-11-0038).
PubMed: 21585270
PLEXdb: browse FG15 experiment data

Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max..
Weston DJ, Karve AA, Gunter LE, Jawdy SS, Yang X, Allen SM, Wullschleger SD.
Plant Cell Environ 2011 May 6
PubMed: 21554326
PLEXdb: browse GM39 experiment data

Transcriptional regulatory programs underlying barley germination and regulatory functions of Gibberellin and abscisic acid..
An YQ, Lin L.
BMC Plant Biol 2011 Jun 13;11:105.
PubMed: 21668981
PLEXdb: browse BB106 experiment data

Identification of differentially expressed genes associated with semigamy in Pima cotton (Gossypium barbadense L.) through comparative microarray analysis..
Curtiss J, Rodriguez-Uribe L, Stewart JM, Zhang J.
BMC Plant Biol 2011 Mar 16;11:49.
PubMed: 21410961
PLEXdb: browse GO3 experiment data

Quantitative and Qualitative Stem Rust Resistance Factors in Barley Are Associated with Transcriptional Suppression of Defense Regulons..
Moscou MJ, Lauter N, Steffenson B, Wise RP
PLoS Genet 7(7): e1002208. doi:10.1371/journal.pgen.1002208 .
PLEXdb: browse BB64 experiment data

Novel aspects of transcriptional regulation in the winter survival and maintenance mechanism of poplar..
Ko JH, Prassinos C, Keathley D, Han KH.
Tree Physiol 2011 Feb;31(2):208-25.
PubMed: 21383024
PLEXdb: browse PT30 experiment data

Compatible GLRaV-3 viral infections affect berry ripening decreasing sugar accumulation and anthocyanin biosynthesis in Vitis vinifera..
Andrea Vega, Rodrigo A. Gutiérrez, Alvaro Peña-Neira, Grant R. Cramer, Patricio Arce-Johnson
PLEXdb: browse VV28 experiment data

Transcriptome phase distribution analysis reveals diurnal regulated biological processes and key pathways in rice flag leaves and seedling leaves..
Xu W, Yang R, Li M, Xing Z, Yang W, Chen G, Guo H, Gong X, Du Z, Zhang Z, Hu X, Wang D, Qian Q, Wang T, Su Z, Xue Y.
PLoS One 2011 Mar 2;6(3):e17613.
PubMed: 21407816
PLEXdb: browse OS64 experiment data

Genome-scale analysis and comparison of gene expression profiles in developing and germinated pollen in Oryza sativa..
Wei LQ, Xu WY, Deng ZY, Su Z, Xue Y, Wang T.
BMC Genomics 2010 May 28;11:338.
PubMed: 20507633
PLEXdb: browse OS63 experiment data

Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice.
Deveshwar P, Bovill WD, Sharma R, Able JA, Kapoor S.
BMC Plant Biol 2011 May 9;11:78.
PubMed: 21554676
PLEXdb: browse OS62 experiment data

Intraspecific variation in the Populus balsamifera drought transcriptome..
Hamanishi ET, Raj S, Wilkins O, Thomas BR, Mansfield SD, Plant AL, Campbell MM.
Plant Cell Environ 2010 Oct;33(10):1742-55. PMID: 20525001.
PubMed: 20525001
PLEXdb: browse PT23 experiment data

An expression database for roots of the model legume Medicago truncatula under salt stress..
Li D, Su Z, Dong J, Wang T.
BMC Genomics 2009 Nov 11;10:517.
PubMed: 19906315
PLEXdb: browse ME6 experiment data

The Phytophthora sojae avirulence locus Avr3c encodes a multi-copy RXLR effector with sequence polymorphisms among pathogen strains..
Dong S, Qutob D, Tedman-Jones J, Kuflu K, Wang Y, Tyler BM, Gijzen M.
PLoS One 2009;4(5):e5556.
PubMed: 19440541
PLEXdb: browse GM27 experiment data

Genotype and time of day shape the Populus drought response..
Wilkins O, Waldron L, Nahal H, Provart NJ, Campbell MM.
Plant J 2009 Nov;60(4):703-15.
PubMed: 19682285
PLEXdb: browse PT22 experiment data

Transcript profiling of two alfalfa genotypes with contrasting cell wall composition in stems using a cross-species platform: optimizing analysis by masking biased probes..
S Samuel Yang, Wayne Wenzhong Xu, Mesfin Tesfaye, JoAnn FS Lamb, Hans-Joachim G Jung, Kathryn A VandenBosch, Carroll P Vance, and John W Gronwald.
BMC Genomics 2010 May 24;11:323.
PubMed: 20497574
PLEXdb: browse ME8 experiment data

Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection..
Libault M, Farmer A, Brechenmacher L, Drnevich J, Langley RJ, Bilgin DD, Radwan O, Neece DJ, Clough SJ, May GD, Stacey G.
Plant Physiol 2010 Feb;152(2):541-52.
PubMed: 19933387
PLEXdb: browse GM38 experiment data

Transcriptome analysis of the barley nec3 mutant reveals a potential link with abiotic stress response related signaling pathways..
Keisa A, Brueggeman R, Drader T, Kleinhofs A, Rostoks N.
Environmental Experimental Biol 2010; 8:1-16.
PLEXdb: browse BB105 experiment data

Significance of light, sugar, and amino acid supply for diurnal gene regulation in developing barley caryopses..
Mangelsen E, Wanke D, Kilian J, Sundberg E, Harter K, Jansson C.
Plant Physiol 2010 May;153(1):14-33.
PubMed: 20304969
PLEXdb: browse BB104 experiment data

Transcriptional Responses to Gibberellin and Abscisic Acid in Barley Aleurone..
Kegui Chen and Yong-Qiang Charles An.
Journal of Integrative Plant Biology, Volume 48 Issue 5, Pages 591 - 612.
PLEXdb: browse BB103 experiment data

RNA profiling of fusarium head blight-resistant wheat addition lines containing the Thinopyrum elongatum chromosome 7E..
Wang, J. -R., Wang, L., Gulden, S., Rocheleau, H., Balcerzak, M., Hattori, J., Cao, W., Han, F., Zheng, Y. -L., Fedak, G. and Ouellet, T.
Canadian Journal of Plant Pathology, Volume 32, Issue 2 April 2010, pages 188 - 214. DOI: 10.1080/07060661003740512
PLEXdb: browse GM35 experiment data
browse TA35 experiment data

Expression of the stress-related genes for glutathione S-transferase and ascorbate peroxidase in the most-glycinin-deficient soybean cultivar Tousan205 during seed maturation..
Narikawa T, Tamura T, Yagasaki K, Terauchi K, Sanmiya K, Ishimaru Y, Abe K, Asakura T.
Biosci Biotechnol Biochem 2010 Sep 23;74(9):1976-9.
PubMed: 20834138
PLEXdb: browse GM34 experiment data

Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors..
Ge Y, Li Y, Lv DK, Bai X, Ji W, Cai H, Wang AX, Zhu YM.
Funct Integr Genomics 2010 Oct 12.
PubMed: 20938706
PLEXdb: browse GM32 experiment data

The Circadian Clock-controlled Transcriptome of Developing Soybean Seeds..
Karen A. Hudson
The Plant Genome, Jul 2010; 3: 3 - 13. doi: 10.3835/?plantgenome2009.08.0025
PLEXdb: browse GM31 experiment data

Transcript profiling of common bean (Phaseolus vulgaris L.) using the GeneChip Soybean Genome Array: optimizing analysis by masking biased probes..
Yang SS, Valdés-López O, Xu WW, Bucciarelli B, Gronwald JW, Hernández G, Vance CP.
BMC Plant Biol 2010 May 7;10:85.
PubMed: 20459672
PLEXdb: browse GM30 experiment data

Mechanisms of magnesium amelioration of aluminum toxicity in soybean at the gene expression level..
Duressa D, Soliman KM, Chen D.
Genome 2010 Oct;53(10):787-97.
PubMed: 20962885
PLEXdb: browse GM29 experiment data

Biphasic gene expression changes elicited by Phakopsora pachyrhizi in soybean correlate with fungal penetration and haustoria formation.
Schneider KT, van de Mortel M, Bancroft TJ, Braun E, Nettleton D, Nelson RT, Frederick RD, Baum TJ, Graham MA, Whitham SA.
Plant Physiol. 2011 Sep;157(1):355-71.
PubMed: 21791600
PLEXdb: browse GM36 experiment data

Loss-of-function of DELLA protein SLN1 activates GA signaling in barley aleurone.
Kegui Chen, Shulan Tian, Brian S. Yandell, Shawn M. Kaeppler and Yong-qiang Charles An
Acta Physiologiae Plantarum. doi:10.1007/s11738-010-0464-3.
PLEXdb: browse BB103 experiment data

Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment..
Ge Y, Li Y, Zhu YM, Bai X, Lv DK, Guo D, Ji W, Cai H.
BMC Plant Biol 2010 Jul 26;10:153.
PubMed: 20653984
PLEXdb: browse GM26 experiment data
browse GM28 experiment data

Identification of rhizome-specific genes by genome-wide differential expression Analysis in Oryza longistaminata..
Hu F, Wang D, Zhao X, Zhang T, Sun H, Zhu L, Zhang F, Li L, Li Q, Tao D, Fu B, Li Z.
BMC Plant Biol 2011 Jan 24;11(1):18.
PubMed: 21261937
PLEXdb: browse OS57 experiment data

Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicola..
Zhou YL, Xu MR, Zhao MF, Xie XW, Zhu LH, Fu BY, Li ZK.
BMC Genomics 2010 Feb 1;11:78.
PubMed: 20122142
PLEXdb: browse OS53 experiment data

Cross-kingdom comparison of transcriptomic adjustments to low-oxygen stress highlights conserved and plant-specific responses..
Mustroph A, Lee SC, Oosumi T, Zanetti ME, Yang H, Ma K, Yaghoubi-Masihi A, Fukao T, Bailey-Serres J.
Plant Physiol 2010 Mar;152(3):1484-500.
PubMed: 20097791
PLEXdb: browse OS52 experiment data

Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.)..
Pandit A, Rai V, Bal S, Sinha S, Kumar V, Chauhan M, Gautam RK, Singh R, Sharma PC, Singh AK, Gaikwad K, Sharma TR, Mohapatra T, Singh NK.
Mol Genet Genomics 2010 Aug;284(2):121-36.
PubMed: 20602115
PLEXdb: browse OS50 experiment data

Identification of candidate genes for grain number in rice (Oryza sativa L.)..
Deshmukh R, Singh A, Jain N, Anand S, Gacche R, Singh A, Gaikwad K, Sharma T, Mohapatra T, Singh N.
Funct Integr Genomics 2010 Aug;10(3):339-47.
PubMed: 20376514
PLEXdb: browse OS49 experiment data

Transcriptome analysis of high-temperature stress in developing barley caryopses: early stress responses and effects on storage compound biosynthesis..
Mangelsen E, Kilian J, Harter K, Jansson C, Wanke D, Sundberg E.
Mol Plant 2011 Jan;4(1):97-115.
PubMed: 20924027
PLEXdb: browse BB102 experiment data

Rice expression atlas in reproductive development..
Fujita M, Horiuchi Y, Ueda Y, Mizuta Y, Kubo T, Yano K, Yamaki S, Tsuda K, Nagata T, Niihama M, Kato H, Kikuchi S, Hamada K, Mochizuki T, Ishimizu T, Iwai H, Tsutsumi N, Kurata N.
Plant Cell Physiol 2010 Dec;51(12):2060-81.
PubMed: 21062870
PLEXdb: browse OS46 experiment data
browse OS43 experiment data
browse OS44 experiment data
browse OS45 experiment data
browse OS42 experiment data

Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress..
Walia H, Wilson C, Ismail AM, Close TJ, Cui X.
BMC Genomics 2009 Aug 25;10:398.
PubMed: 19706179
PLEXdb: browse OS41 experiment data

Transcriptional profiling of rice leaves undergoing a hypersensitive response like reaction induced by Xanthomonas oryzae pv. oryzae cellulase..
Gopaljee Jha, Hitendra Kumar Patel, Madhumita Dasgupta, Ramesh Palaparthi and R. V. Sonti.
Rice 2010. 3: 1-21. DOI: 10.1007/s12284-009-9033-z
PLEXdb: browse OS40 experiment data

Transcriptional profile of maize roots under acid soil growth..
Mattiello L, Kirst M, da Silva FR, Jorge RA, Menossi M.
BMC Plant Biol 2010 Sep 9;10:196.
PubMed: 20828383
PLEXdb: browse ZM33 experiment data

Aneuploidy causes tissue-specific qualitative changes in global gene expression patterns in maize..
Makarevitch I, Harris C.
Plant Physiol 2010 Feb;152(2):927-38.
PubMed: 20018594
PLEXdb: browse ZM31 experiment data

Genome-wide transcriptome analysis of two maize inbred lines under drought stress..
Zheng J, Fu J, Gou M, Huai J, Liu Y, Jian M, Huang Q, Guo X, Dong Z, Wang H, Wang G.
Plant Mol Biol 2010 Mar;72(4-5):407-21.
PubMed: 19953304
PLEXdb: browse ZM30 experiment data

A cation/proton-exchanging protein is a candidate for the barley NecS1 gene controlling necrosis and enhanced defense response to stem rust..
Zhang L, Lavery L, Gill U, Gill K, Steffenson B, Yan G, Chen X, Kleinhofs A.
Theor Appl Genet. 2009 Jan;118(2):385-97. Epub 2008 Oct 28.
PubMed: 18956175
PLEXdb: browse BB54 experiment data

Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean.
Bolon YT, Joseph B, Cannon SB, Graham MA, Diers BW, Farmer AD, May GD, Muehlbauer GJ, Specht JE, Tu ZJ, Weeks N, Xu WW, Shoemaker RC, Vance CP.
BMC Plant Biol. 2010 Mar 3;10:41
PubMed: 20199683
PLEXdb: browse GM11 experiment data

The seed composition of Arabidopsis mutants for the group 3 sulfate transporters indicates a role in sulfate translocation within developing seeds..
Hélène Zuber, Jean-Claude Davidian, Grégoire Aubert, Delphine Aimé, Maya Belghazi, Raphaël Lugan, Dimitri Heintz, Markus Wirtz, Rüdiger Hell, Richard Thompson and Karine Gallardo.
Plant Physiol 2010 Oct;154(2):913-26.
PubMed: 20702726
PLEXdb: browse AT107 experiment data

Predictive network modeling of the high-resolution dynamic plant transcriptome in response to nitrate..
Krouk G, Mirowski P, Lecun Y, Shasha DE, Coruzzi GM.
Genome Biol 2010 Dec 23;11(12):R123.
PubMed: 21182762
PLEXdb: browse AT108 experiment data

The seed composition of Arabidopsis mutants for the group 3 sulfate transporters indicates a role in sulfate translocation within developing seeds..
Zuber H, Davidian JC, Aubert G, Aimé D, Belghazi M, Lugan R, Heintz D, Wirtz M, Hell R, Thompson R, Gallardo K.
Plant Physiol 2010 Oct;154(2):913-26.
PubMed: 20702726
PLEXdb: browse AT106 experiment data

Blufensin1 negatively impacts basal defense in response to barley powdery mildew.
Meng, Y, MJ Moscou, and RP Wise
Plant Physiology 149: 271-285
PubMed: 19005086
PLEXdb: browse BB101 experiment data

Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors.
Le BH, Cheng C, Bui AQ, Wagmaister JA, Henry KF, Pelletier J, Kwong L, Belmonte M, Kirkbride R, Horvath S, Drews GN, Fischer RL, Okamuro JK, Harada JJ, Goldberg RB
Proc Natl Acad Sci U S A 2010 May 4;107(18):8063-70
PubMed: 20385809
PLEXdb: browse AT101 experiment data

Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors..
Le BH, Cheng C, Bui AQ, Wagmaister JA, Henry KF, Pelletier J, Kwong L, Belmonte M, Kirkbride R, Horvath S, Drews GN, Fischer RL, Okamuro JK, Harada JJ, Goldberg RB.
Proc Natl Acad Sci U S A 2010 May 4;107(18):8063-70.
PubMed: 20385809
PLEXdb: browse AT102 experiment data

Genome-wide atlas of transcription during maize development.
Sekhon RS, Lin H, Childs KL, Hansey CN, Robin Buell C, de Leon N, Kaeppler SM
Plant J. 2011 Feb 7.[Epub ahead of print].
PubMed: 21299659
PLEXdb: browse ZM29 experiment data

Endogenous overexpression of Populus MYB186 increases trichome density, improves insect pest resistance, and impacts plant growth..
Plett JM, Wilkins O, Campbell MM, Ralph SG, Regan S.
Plant J 2010 Nov;64(3):419-32.
PubMed: 20807210
PLEXdb: browse PT21 experiment data

Transcriptome responses to aluminum stress in roots of aspen (Populus tremula)..
Grisel N, Zoller S, Künzli-Gontarczyk M, Lampart T, Münsterkötter M, Brunner I, Bovet L, Métraux JP, Sperisen C.
BMC Plant Biol 2010 Aug 23;10:185.
PubMed: 20727216
PLEXdb: browse PT18 experiment data

The transcription factor FgStuAp influences spore development, pathogenicity, and secondary metabolism in Fusarium graminearum.
Lysoe, E., Pasquali, M., Breakspear, A., and Kistler, H.C.
Mol Plant Microbe Interact 24: 54-67(2011)
PubMed: 20879840
PLEXdb: browse FG13 experiment data

Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement.
Maria Munoz-Amatriain, Yanwen Xiong, Mark R Schmitt, Hatice Bilgic, Allen D Budde, Shiaoman Chao, Kevin P Smith, Gary J Muehlbauer
BMC Genomics 11:653 (DOI: 10.1186/1471-2164-11-653 ).
PubMed: 21092286
PLEXdb: browse BB91 experiment data

Alternative splicing and gene duplication differentially shaped the regulation of isochorismate synthase in Populus and Arabidopsis..
Yuan Y, Chung JD, Fu X, Johnson VE, Ranjan P, Booth SL, Harding SA, Tsai CJ.
Proc Natl Acad Sci U S A 2009 Dec 22;106(51):22020-5.
PubMed: 19996170
PLEXdb: browse PT15 experiment data

Gibberellins regulate lateral root formation in Populus through interactions with auxin and other hormones..
Gou J, Strauss SH, Tsai CJ, Fang K, Chen Y, Jiang X, Busov VB.
Plant Cell 2010 Mar;22(3):623-39.
PubMed: 20354195
PLEXdb: browse PT14 experiment data

Global gene expression responses to waterlogging in roots and leaves of cotton (Gossypium hirsutum L.)..
Christianson JA, Llewellyn DJ, Dennis ES, Wilson IW.
Plant Cell Physiol 2010 Jan;51(1):21-37.
PubMed: 19923201
PLEXdb: browse GO1 experiment data

WRKY72-type transcription factors contribute to basal immunity in tomato and Arabidopsis as well as gene-for-gene resistance mediated by the tomato R gene Mi-1..
Bhattarai KK, Atamian HS, Kaloshian I, Eulgem T.
Plant J 2010 Jul;63(2):229-40.
PubMed: 20409007
PLEXdb: browse AT100 experiment data

An orange ripening mutant links plastid NAD(P)H dehydrogenase complex activity to central and specialized metabolism during tomato fruit maturation..
Nashilevitz S, Melamed-Bessudo C, Izkovich Y, Rogachev I, Osorio S, Itkin M, Adato A, Pankratov I, Hirschberg J, Fernie AR, Wolf S, Usadel B, Levy AA, Rumeau D, Aharoni A.
Plant Cell 2010 Jun;22(6):1977-97.
PubMed: 20571113
PLEXdb: browse LE11 experiment data

Tomato root transcriptome response to a nitrogen-enriched soil patch..
Ruzicka DR, Barrios-Masias FH, Hausmann NT, Jackson LE, Schachtman DP.
Plant Biol 2010 Apr 27;10:75.
PubMed: 20423508
PLEXdb: browse LE10 experiment data

Comparative transcriptomic profiling of a salt-tolerant wild tomato species and a salt-sensitive tomato cultivar..
Wei Sun, Xinna Xu, Huishan Zhu, Aihua Liu, Lei Liu, Junming Li, and Xuejun Hua.
Plant Cell Physiol 2010 Jun;51(6):997-1006.
PubMed: 20410049
PLEXdb: browse LE6 experiment data

Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module..
Ozaki S, Ogata Y, Suda K, Kurabayashi A, Suzuki T, Yamamoto N, Iijima Y, Tsugane T, Fujii T, Konishi C, Inai S, Bunsupa S, Yamazaki M, Shibata D, Aoki K.
DNA Res 2010;17(2):105-16.
PubMed: 20130013
PLEXdb: browse LE7 experiment data

Gene regulation in parthenocarpic tomato fruit..
Martinelli F, Uratsu SL, Reagan RL, Chen Y, Tricoli D, Fiehn O, Rocke DM, Gasser CS, Dandekar AM.
J Exp Bot 2009;60(13):3873-90.
PubMed: 19700496
PLEXdb: browse LE5 experiment data

A central role of abscisic acid in drought stress protection of Agrobacterium-induced tumors on Arabidopsis.
Efetova M, Zeier J, Riederer M, Lee CW, Stingl N, Mueller M, Hartung W, Hedrich R, Deeken R.
Plant Physiol 2007 Nov;145(3):853-62
PubMed: 17827272

The Arabidopsis transcription factor WRKY27 influences wilt disease symptom development caused by Ralstonia solanacearum. Plant J. 56, 935-947..
Mukhtar, S.M., Deslandes, L., Auriac, M.-C., Marco, Y., and Somssich, I.E.
Plant J. 56:935-947(2008)
PubMed: 18702671
PLEXdb: browse AT46 experiment data

Tryptophan-derived metabolites are required for antifungal defense in the Arabidopsis mlo2 mutant..
Consonni C, Bednarek P, Humphry M, Francocci F, Ferrari S, Harzen A, Ver Loren van Themaat E, Panstruga R.
Plant Physiol. 2010 Mar;152(3):1544-61. Epub 2009 Dec 18.
PubMed: 20023151
PLEXdb: browse AT89 experiment data

A MYB transcription factor regulates very-long-chain fatty acid biosynthesis for activation of the hypersensitive cell death response in Arabidopsis.
Raffaele S, Vailleau F, Léger A, Joubès J, Miersch O, Huard C, Blée E, Mongrand S, Domergue F, Roby D
Plant Cell. 2008 Mar;20(3):752-67. Epub 2008 Mar 7
PubMed: 18326828
PLEXdb: browse AT87 experiment data

An integrated view of gene expression and solute profiles of Arabidopsis tumors: a genome-wide approach.
Deeken R, Engelmann JC, Efetova M, Czirjak T, Müller T, Kaiser WM, Tietz O, Krischke M, Mueller MJ, Palme K, Dandekar T, Hedrich R
Plant Cell 2006 Dec;18(12):3617-34
PubMed: 17172353
PLEXdb: browse AT86 experiment data

Myzus persicae (green peach aphid) salivary components induce defence responses in Arabidopsis thaliana.
De Vos M, Jander G
Plant Cell Environ 2009 Nov;32(11):1548-60
PubMed: 19558622
PLEXdb: browse AT83 experiment data

Differential innate immune signalling via Ca(2+) sensor protein kinases.
Boudsocq M, Willmann MR, McCormack M, Lee H, Shan L, He P, Bush J, Cheng SH, Sheen J
Nature 2010 Mar 18;464(7287):418-22
PubMed: 20164835
PLEXdb: browse AT82 experiment data

Differential innate immune signalling via Ca(2+) sensor protein kinases.
Boudsocq M, Willmann MR, McCormack M, Lee H et al
Nature 2010 Mar 18;464(7287):418-22
PubMed: 20164835
PLEXdb: browse AT81 experiment data

Laser microdissection of Arabidopsis cells at the powdery mildew infection site reveals site-specific processes and regulators.
Chandran D, Inada N, Hather G, Kleindt CK et al
Proc Natl Acad Sci U S A 2010 Jan 5;107(1):460-5
PubMed: 20018666
PLEXdb: browse AT80 experiment data

Arabidopsis transcriptome changes in response to phloem-feeding silverleaf whitefly nymphs. Similarities and distinctions in responses to aphids.
Kempema LA, Cui X, Holzer FM, Walling LL
Plant Physiol 2007 Feb;143(2):849-65
PubMed: 17189325
PLEXdb: browse AT63 experiment data

The mediator complex subunit PFT1 is a key regulator of jasmonate-dependent defense in Arabidopsis.
Kidd BN, Edgar CI, Kumar KK, Aitken EA et al
Plant Cell 2009 Aug;21(8):2237-52
PubMed: 19671879
PLEXdb: browse AT79 experiment data

Agrobacterium tumefaciens promotes tumor induction by modulating pathogen defense in Arabidopsis thaliana.
Lee CW, Efetova M, Engelmann JC, Kramell R, Wasternack C, Ludwig-Mller J, Hedrich R, Deeken R.
Plant Cell. 2009 Sep;21(9):2948-62. Epub 2009 Sep 30.
PubMed: 19794116
PLEXdb: browse AT77 experiment data
browse AT86 experiment data

A central role of abscisic acid in drought stress protection of Agrobacterium-induced tumors on Arabidopsis.
Efetova M, Zeier J, Riederer M, Lee CW, Stingl N, Mueller M, Hartung W, Hedrich R, Deeken R.
Plant Physiol 2007 Nov;145(3):853-62.
PubMed: 17827272
PLEXdb: browse AT76 experiment data

An integrated view of gene expression and solute profiles of Arabidopsis tumors: a genome-wide approach.
Deeken R, Engelmann JC, Efetova M, Czirjak T, Mller T, Kaiser WM, Tietz O, Krischke M, Mueller MJ, Palme K, Dandekar T, Hedrich R.
Plant Cell 2006 Dec;18(12):3617-34
PubMed: 17172353
PLEXdb: browse AT76 experiment data
browse AT77 experiment data

The synthetic elicitor 3,5-dichloroanthranilic acid induces NPR1-dependent and NPR1-independent mechanisms of disease resistance in Arabidopsis.
Knoth C, Salus MS, Girke T, Eulgem T
Plant Physiol 2009 May;150(1):333-47
PubMed: 19304930
PLEXdb: browse AT75 experiment data

Temporal global expression data reveal known and novel salicylate-impacted processes and regulators mediating powdery mildew growth and reproduction on Arabidopsis.
Chandran D, Tai YC, Hather G, Dewdney J et al
Plant Physiol 2009 Mar;149(3):1435-51
PubMed: 19176722
PLEXdb: browse AT74 experiment data

Flg22 regulates the release of an ethylene response factor substrate from MAP kinase 6 in Arabidopsis thaliana via ethylene signaling.
Bethke G, Unthan T, Uhrig JF, Pöschl Y et al
Proc Natl Acad Sci U S A 2009 May 12;106(19):8067-72
PubMed: 19416906
PLEXdb: browse AT72 experiment data
browse AT73 experiment data

A LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis.
Wan J, Zhang XC, Neece D, Ramonell KM et al
Plant Cell 2008 Feb;20(2):471-81
PubMed: 18263776
PLEXdb: browse AT67 experiment data

Dual regulation role of GH3.5 in salicylic acid and auxin signaling during Arabidopsis-Pseudomonas syringae interaction.
Zhang Z, Li Q, Li Z, Staswick PE et al
Plant Physiol 2007 Oct;145(2):450-64
PubMed: 17704230
PLEXdb: browse AT64 experiment data

not specified at original website.
PLEXdb: browse AT59 experiment data

Signal signature anome changes of Arabidopsis during pathogen and insect attack..
De Vos M, Van Oosten VR, Van Poecke RM, Van Pelt JA et al.
Mol. Plant Microbe Interact. 18(9):923-37(2005)
PubMed: 16167763
PLEXdb: browse AT49 experiment data

The Populus homeobox gene ARBORKNOX2 regulates cell differentiation during secondary growth..
Du J, Mansfield SD, Groover AT.
Plant J. 2009 Dec;60(6):1000-14. Epub
PubMed: 19737362

A novel regulatory system in plants involving medium-chain fatty acids..
Hunzicker GM.
Planta 2009 Dec;231(1):143-53.
PubMed: 19876644
PLEXdb: browse AT44 experiment data

Transcriptome analysis of the barley-deoxynivalenol interaction: evidence for a role of glutathione in deoxynivalenol detoxification.
Gardiner, S.A., J. Boddu, F. Berthiller, C. Hametner, R. Stupar, G. Adam, and G.J. Muehlbauer.
Mol. Plant-Microbe Interact. 23(7):962-976(2010)
PubMed: 20521958
PLEXdb: browse BB62 experiment data

Triacylglyceride metabolism by Fusarium graminearum during colonization and sexual development on wheat.
Guenther, John C, Hallen-Adams, Heather E, Buecking, H, Shachar-Hill, Y, and Trail, F
Molecular Plant Microbe Interactions 22(12):1492-503(2009).
PubMed: 19888815
PLEXdb: browse FG16 experiment data

Phases of Infection and Gene Expression of Fusarium graminearum During Crown Rot Disease of Wheat.
Amber E. Stephens, Donald M. Gardiner, Rosemary G. White, Alan L. Munn and John M. Manners
PLEXdb: browse FG12 experiment data

A partial chromosome deletion caused by random plasmid integration resulted in a reduced virulence phenotype in Fusarium graminearum.
Thomas K. Baldwin, Iffa Gaffoor, John Antoniw, Corrie Andries, John Guenther, Martin Urban, Heather E. Hallen-Adams, John Pitkin, Kim E. Hammond-Kosack, Frances Trail
Molecular Plant Microbe Interactions

ODDSOC2 is a MADS box floral repressor that is down-regulated by vernalization in temperate cereals.
Aaron G. Greenup, Shahryar Sasani, Sandra N. Oliver, Mark J. Talbot, Elizabeth S. Dennis, Megan N. Hemming and Ben Trevaskis
Plant Physiol. 2010 Apr 29. [Epub ahead of print]
PubMed: 20431086
PLEXdb: browse BB93 experiment data

Not in GEO.
PLEXdb: browse VV19 experiment data

Expression profiling and functional analysis of Populus WRKY23 reveals a regulatory role in defense..
Levée V, Major I, Levasseur C, Tremblay L, MacKay J, Séguin A.
New Phytol. 2009;184(1):48-70. Epub 2009 Jul 21.
PubMed: 19674332
PLEXdb: browse PT7 experiment data

A comprehensive transcriptomic analysis of the effect of silicon on wheat plants under control and pathogen stress conditions..
Chain F, Côté-Beaulieu C, Belzile F, Menzies JG, Bélanger RR.
Mol Plant Microbe Interact. 2009 Nov;22(11):1323-30.
PubMed: 19810802
PLEXdb: browse TA34 experiment data

Multilevel regulation and signalling processes associated with adaptation to terminal drought in wild emmer wheat .
Tamar Krugman, Vronique Chagu, Zvi Peleg, Sandrine Balzergue, Jrmy Just, Abraham B. Korol, Eviatar Nevo, Yehoshua Saranga, Boulos Chalhoub and Tzion Fahima
Functional and Integrative Genomics. 2010.
PLEXdb: browse TA33 experiment data

A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control..
Huang XY, Chao DY, Gao JP, Zhu MZ, Shi M, Lin HX.
Genes Dev 2009 Aug 1;23(15):1805-17.
PubMed: 19651988
PLEXdb: browse OS34 experiment data

A dynamic gene expression atlas covering the entire life cycle of rice.
Wang L, Xie W, Chen Y, Tang W, Yang J, Ye R, Liu L, Lin Y, Xu C, Xiao J, Zhang Q.
The Plant Journal (2010) 61, 752–766
PubMed: 20003165
PLEXdb: browse OS32 experiment data

DEP and AFO regulate reproductive habit in rice..
Wang K, Tang D, Hong L, Xu W, Huang J, Li M, Gu M, Xue Y, Cheng Z.
PLoS Genet 2010 Jan 22;6(1):e1000818.
PubMed: 20107517
PLEXdb: browse OS33 experiment data

Structural and functional characterization of a winter malting barley .
Mara Muoz-Amatrian , L. Cistu, Y. Xiong, H. Bilgic, A. D. Budde, M. R. Schmitt, K. P. Smith, P. M. Hayes and G. J. Muehlbauer
Theoretical and Applied Genetics 120(5): 971-984 (2010)
PubMed: 19960335
PLEXdb: browse BB76 experiment data

Physiological and transcriptome analysis of iron and phosphorus interaction in rice seedlings.
Zheng L, Huang F, Narsai R, Wu J, Giraud E, He F, Cheng L, Wang F, Wu P, Whelan J, Shou H
Plant Physiol. 2009 Sep;151(1):262-74. Epub 2009 Jul 15.
PubMed: 19605549
PLEXdb: browse OS31 experiment data

Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools..
Sreenivasulu N, Usadel B, Winter A, Radchuk V, Scholz U, Stein N, Weschke W, Strickert M, Close TJ, Stitt M, Graner A, Wobus U
Plant Physiol 2008 Apr;146(4):1738-58.
PubMed: 18281415
PLEXdb: browse BB85 experiment data
browse BB86 experiment data

Differentially expressed genes during malting and correlation with malting quality phenotypes in barley (Hordeum vulgare L.)..
Lapitan NL, Hess A, Cooper B, Botha AM et al.
Theor Appl Genet 2009 Mar;118(5):937-52.
PubMed: 19132335
PLEXdb: browse BB87 experiment data

SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip..
Fujisawa H, Horiuchi Y, Harushima Y, Takada T et al.
BMC Bioinformatics 2009 May 6;10:131.
PubMed: 19419536
PLEXdb: browse OS29 experiment data

Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice..
Jain M, Khurana JP.
FEBS J 2009 Jun;276(11):3148-62.
PubMed: 19490115
PLEXdb: browse OS28 experiment data

Glycinebetaine-induced water-stress tolerance in codA-expressing transgenic indica rice is associated with up-regulation of several stress responsive genes..
Kathuria H, Giri J, Nataraja KN, Murata N et al.
Plant Biotechnol J 2009 Aug;7(6):512-26
PubMed: 19490479
PLEXdb: browse OS27 experiment data

Transcriptome Analysis of a Wheat Near-Isogenic Line Pair Carrying Fusarium Head Blight-Resistant and -Susceptible Alleles.
Haiyan Jia, Seungho Cho, Gary J. Muehlbauer
Molecular Plant-Microbe Interactions 22(11):1366-1378 (2009).
PLEXdb: browse TA20 experiment data

Wild barley expresses distinct sets of genes in response to pathogens of different trophic lifestyles..
Millett, B.P., Y. Xiong, S. Dahl, B.J. Steffenson, G.J. Muehlbauer.
Physiol. & Mol. Plant Path. (2009)
PLEXdb: browse BB61 experiment data

Drought response in the spikes of barley: gene expression in the lemma, palea, awn, and seed..
Tilahun Abebe1, Kalpalatha Melmaiee1, Virginia Berg and Roger P. Wise.
Functional & Integrative Genomics : epub ahead of print (Nov 2009).
PLEXdb: browse BB89 experiment data

Comparative Transcriptional Profiling Established the Awn as the Major Photosynthetic Organ of the Barley Spike While the Lemma and the Palea Primarily Protect the Seed .
Tilahun Abebe, Roger P. Wise, and Ronald W. Skadsen.
Plant Genome 2:247-259 (2009).
PLEXdb: browse BB73 experiment data

Transcript-Based Cloning of RRP46, a Regulator of rRNA Processing and R Gene-Independent Cell Death in Barley-Powdery Mildew Interactions. .
Xi L, Moscou MJ, Meng Y, Xu W, Caldo RA, Shaver M, Nettleton D, Wise RP.
The Plant Cell 21:3280-3295 (2009).
PubMed: 19861556
PLEXdb: browse BB46 experiment data

Expansion and diversification of the Populus R2R3-MYB family of transcription factors.
Wilkins O, Nahal H, Foong J, Provart NJ et al
Plant Physiol 2009 Feb;149(2):981-93
PubMed: 19091872
PLEXdb: browse PT2 experiment data

Wheat blast: histopathology and transcriptome reprogramming in response to adapted and nonadapted Magnaporthe isolates .
Hale A. Tufan, Graham R. D. McGrann, Andreas Magusin, Jean-Benoit Morel, Lucie Mich, Lesley A. Boyd
New Phytologist Volume 184(2):473-484 (2009).
PLEXdb: browse TA24 experiment data

Gene expression in grapevine cultivars in response to Bois Noir phytoplasma infection..
Albertazzi G., Caffagni A., Milc J.A., Francia E., Roncaglia E., Ferrari F., Tagliafico E., Stefani E., Pecchioni N.(2009)
Plant Science 176: 792-804 .
PLEXdb: browse VV14 experiment data

Ripening-Regulated Susceptibility of Tomato Fruit to Botrytis cinerea Requires NOR But Not RIN or Ethylene.
Cantu D, Blanco-Ulate B, Yang L, Labavitch JM et al
Plant Physiol 2009 Jul;150(3):1434-49
PubMed: 19465579
PLEXdb: browse LE3 experiment data

Novel Genes of Fusarium graminearum That Negatively Regulate Deoxynivalenol Production and Virulence.
D. M. Gardiner, K. Kazan, and J. M. Manners.
Mol Plant Microbe Interact. 2009 Dec;22(12):1588-600.
PubMed: 19888824
PLEXdb: browse FG14 experiment data

Lr34-mediated leaf rust resistance in wheat: transcript profiling reveals a high energetic demand supported by transient recruitment of multiple metabolic pathways.
Bolton MD, Kolmer JA, Xu WW, Garvin DF
Mol Plant Microbe Interact 2008 Dec;21(12):1515-27
PubMed: 18986248
PLEXdb: browse TA32 experiment data

Gene expression analysis of the wheat response to infection by Fusarium pseudograminearum.
Desmond, O.J., Manners, J.M., Schenk, P.M., Mclean, D.J. and Kazan K
Physiological and Molecular Plant Pathology. doi:10.1016/j.pmpp.2008.12.001
PLEXdb: browse TA31 experiment data

Molecular dissection of variation in carbohydrate metabolism related to water-soluble carbohydrate accumulation in stems of wheat.
Xue GP, McIntyre CL, Jenkins CL, Glassop D et al
Plant Physiol 2008 Feb;146(2):441-54
PubMed: 18083795
PLEXdb: browse TA30 experiment data

Suppression of Soybean Oleosin Produces Micro-Oil Bodies that Aggregate into Oil Body/ER Complexes.
Schmidt, MA and Herman, EM
Molecular Plant Advance Access published on September 15, 2008. doi:10.1093/mp/ssn049
PLEXdb: browse GM22 experiment data

Gene expression analysis in soybean in response to the causal agent of Asian soybean rust (Phakopsora pachyrhizi Sydow) in an early growth stage..
Panthee DR, Yuan JS, Wright DL, Marois JJ et al.
Funct Integr Genomics 2007 Oct;7(4):291-301
PubMed: 17318271
PLEXdb: browse GM12 experiment data

Genome-wide analysis of gene expression in soybean shoot apical meristem.
Haerizadeh F, Wong CE, Singh MB, Bhalla PL
Plant Mol Biol 2009 Apr;69(6):711-27
PubMed: 19115044
PLEXdb: browse GM20 experiment data

Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array.
Das S, Bhat PR, Sudhakar C, Ehlers JD et al
BMC Genomics 2008 Feb 28;9:107
PubMed: 18307807
PLEXdb: browse GM19 experiment data

Molecular processes underlying the floral transition in the soybean shoot apical meristem.
Wong CE, Singh MB, Bhalla PL
Plant J 2009 Mar;57(5):832-45
PubMed: 18980639
PLEXdb: browse GM18 experiment data

The genetics of barley low-tillering mutants: absent lower laterals (als)..
Dabbert T, Okagaki RJ, Cho S, Boddu J, Muehlbauer GJ.
Theor Appl Genet. 2009 May;118(7):1351-60.
PubMed: 19241055
PLEXdb: browse BB47 experiment data

Effect of transgenes on global gene expression in soybean is within the natural range of variation of conventional cultivars.
Cheng KC, Beaulieu J, Iquira E, Belzile FJ et al
J Agric Food Chem 2008 May 14;56(9):3057-6
PubMed: 18433101
PLEXdb: browse GM16 experiment data

A microarray analysis for differential gene expression in the soybean genome using Bioconductor and R.
Gregory Alvord W, Roayaei JA, Quiñones OA, Schneider KT
Brief Bioinform 2007 Nov;8(6):415-31
PubMed: 17906332
PLEXdb: browse GM15 experiment data

Transcriptional analysis of the sweet orange interaction with the citrus canker pathogens Xanthomonas axonopodis pv. citri and Xanthomonas axonopodis pv. aurantifolii..
PubMed: 19018992
PLEXdb: browse CT2 experiment data

Transcriptome profiling in hybrid poplar following interactions with Melampsora rust fungi.
Azaiez A, Boyle B, Levée V, Séguin A
Mol Plant Microbe Interact 2009 Feb;22(2):190-200
PubMed: 19132871
PLEXdb: browse PT1 experiment data

Differential expression of genes in the leaves of sugarcane in response to sugar accumulation.
McCormick A, Cramer M, Watt D
ropical Plant Biology, Volume 1, Number 2, June 2008 , pp. 142-158(17)
PLEXdb: browse SO1 experiment data

Microarray expression analysis of meiosis and microsporogenesis in hexaploid bread wheat.
Crismani W, Baumann U, Sutton T, Shirley N et al
BMC Genomics 2006 Oct 19;7:267
PubMed: 17052357
PLEXdb: browse TA27 experiment data

Barley elicits a similar early basal defence response during host and non-host interactions with Polymyxa root parasites.
Graham R. D. McGrann, Belinda J. Townsend, John F. Antoniw, Michael J. C. Asher, Effie S. Mutasa-Göttgens
European Journal of Plant Pathology 123(1):5-15
PLEXdb: browse BB74 experiment data
browse BB75 experiment data

Genome-wide transcriptional analysis of super-embryogenic Medicago truncatula explant cultures.
Imin N, Goffard N, Nizamidin M, Rolfe BG
BMC Plant Biol 2008 Oct 27;8:110
PubMed: 18950541
PLEXdb: browse ME3 experiment data

Transcriptional profiling of Medicago truncatula meristematic root cells.
Holmes P, Goffard N, Weiller GF, Rolfe BG et al
BMC Plant Biol 2008 Feb 27;8:21
PubMed: 18302802
PLEXdb: browse ME2 experiment data

Gene expression analyses in individual grape (Vitis vinifera L.) berries during ripening initiation reveal that pigmentation intensity is a valid indicator of developmental staging within the cluster.
Lund ST, Peng FY, Nayar T, Reid KE et al
Plant Mol Biol 2008 Oct;68(3):301-15
PubMed: 18642093
PLEXdb: browse VV15 experiment data

Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome.
A Aprile, A M Mastrangelo, A M De Leonardis, G Galiba, E Roncaglia, F Ferrari, L De Bellis, L Turchi, G Giuliano, L Cattivelli
BMC Genomics 2009, 10:279.
PLEXdb: browse TA23 experiment data

Comparative transcriptomics in the Triticeae.
Andreas W Schreiber, Tim Sutton, Rico A Caldo, Elena Kalashyan, Ben Lovell, Gwenda Mayo, Gary J Muehlbauer, Arnis Druka, Robbie Waugh, Roger P Wise, Peter Langridge and Ute Baumann
BMC Genomics 2009, 10:285.
PubMed: 19558723
PLEXdb: browse BB3 experiment data
browse TA3 experiment data

Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion..
Batista R, Saibo N, Lourenço T, Oliveira MM.
Proc Natl Acad Sci U S A 2008 Mar 4;105(9):3640-5
PubMed: 18303117
PLEXdb: browse OS24 experiment data

Highly sensitive and high-throughput analysis of plant hormones using MS-probe modification and liquid chromatography-tandem mass spectrometry: an application for hormone profiling in Oryza sativa.
Kojima M, Kamada-Nobusada T, Komatsu H, Takei K et al
Plant Cell Physiol 2009 Apr 20
PubMed: 19369275
PLEXdb: browse OS23 experiment data

OsLIC, a Novel CCCH-Type Zinc Finger Protein with Transcription Activation, Mediates Rice Architecture via Brassinosteroids Signaling.
Wang L, Xu Y, Zhang C, Ma Q et al
PLoS ONE 2008;3(10):e3521
PubMed: 18953406
PLEXdb: browse OS22 experiment data

Global patterns of gene expression in rice cultivars undergoing a susceptible or resistant interaction with the parasitic plant Striga hermonthica..
Swarbrick PJ, Huang K, Liu G, Slate J et al.
New Phytol 2008 May 26.
PubMed: 18507775
PLEXdb: browse OS19 experiment data

Control of rice grain-filling and yield by a gene with a potential signature of domestication..
Wang E, Wang J, Zhu X, Hao W et al.
Nat Genet 2008 Nov;40(11):1370-4
PubMed: 18820698
PLEXdb: browse OS17 experiment data

Genome-wide gene expression profiling reveals conserved and novel molecular functions of the stigma in rice..
Li M, Xu W, Yang W, Kong Z et al.
Plant Physiol 2007 Aug;144(4):1797-812.
PubMed: 17556504
PLEXdb: browse OS16 experiment data

Down-regulation of a SILENT INFORMATION REGULATOR2-related histone deacetylase gene, OsSRT1, induces DNA fragmentation and cell death in rice..
Huang L, Sun Q, Qin F, Li C et al
Plant Physiol 2007 Jul;144(3):1508-19
PubMed: 17468215
PLEXdb: browse OS15 experiment data

Transcript profiling of the anoxic rice coleoptile..
Lasanthi-Kudahettige R, Magneschi L, Loreti E, Gonzali S et al.
Plant Physiol 2007 May;144(1):218-31
PubMed: 17369434
PLEXdb: browse OS14 experiment data

Overexpression of a type-A response regulator alters rice morphology and cytokinin metabolism..
Hirose N, Makita N, Kojima M, Kamada-Nobusada T et al.
Plant Cell Physiol 2007 Mar;48(3):523-39.
PubMed: 17293362
PLEXdb: browse OS13 experiment data

Overexpression of a type-A response regulator alters rice morphology and cytokinin metabolism..
Hirose N, Makita N, Kojima M, Kamada-Nobusada T et al.
Plant Cell Physiol 2007 Mar;48(3):523-39
PubMed: 17293362
PLEXdb: browse OS12 experiment data

Natural variation for alleles under epigenetic control by the maize chromomethylase zmet2..
Makarevitch I, Stupar RM, Iniguez AL, Haun WJ et al.
Genetics 2007 Oct;177(2):749-60.
PubMed: 17660570
PLEXdb: browse ZM26 experiment data

Pep1, a secreted effector protein of Ustilago maydis, is required for successful invasion of plant cells..
Doehlemann G, van der Linde K, Assmann D, Schwammbach D et al.
PLoS Pathog 2009 Feb;5(2):e1000290.
PubMed: 19197359
PLEXdb: browse ZM24 experiment data

Profiling expression changes caused by a segmental aneuploid in maize..
Makarevitch I, Phillips RL, Springer NM
BMC Genomics 2008 Jan 10;9:7.
PubMed: 18186930
PLEXdb: browse ZM23 experiment data

Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis..
Stupar RM, Gardiner JM, Oldre AG, Haun WJ et al.
BMC Plant Biol 2008 Apr 10;8:33
PubMed: 18402703
PLEXdb: browse ZM21 experiment data

Nonadditive expression and parent-of-origin effects identified by microarray and allele-specific expression profiling of maize endosperm..
Stupar RM, Hermanson PJ, Springer NM.
Plant Physiol 2007 Oct;145(2):411-25.
PubMed: 17766400
PLEXdb: browse ZM17 experiment data

Nonadditive expression and parent-of-origin effects identified by microarray and allele-specific expression profiling of maize endosperm..
Stupar RM, Hermanson PJ, Springer NM
Plant Physiol 2007 Oct;145(2):411-25.
PubMed: 17766400
PLEXdb: browse ZM16 experiment data

Microarray analysis of the interaction between the aphid Rhopalosiphum padi and host plants reveals both differences and similarities between susceptible and partially resistant barley lines..
Delp G, Gradin T, Ahman I, Jonsson LM.
Mol Genet Genomics 2009 Mar;281(3):233-48.
PubMed: 19085010
PLEXdb: browse BB71 experiment data

Using Genomics to Study Legume Seed Development.
Brandon H. Le, Javier A. Wagmaister , Tomokazu Kawashima, Anhthu Q. Bui, John J. Harada, and Robert B. Goldberg
Plant Physiology
PLEXdb: browse GM10 experiment data

Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid..
Stupar RM, Springer NM
Gentics 2006 Aug;173(4):2199-210
PubMed: 16702414
PLEXdb: browse ZM12 experiment data

Susceptibility of rice to the blast fungus, Magnaporthe grisea..
Ribot C, Hirsch J, Balzergue S, Tharreau D, Nottghem JL, Lebrun MH, Morel JB.
J Plant Physiol. 2008 Jan;165(1):114-24
PubMed: 17905473
PLEXdb: browse OS7 experiment data

Transcriptome Analysis of Cold Acclimation in Barley Albina and Xantha Mutants.
Jan T. Svensson, Cristina Crosatti, Chiara Campoli, Roberto Bassi, Antonio Michele Stanca, Timothy J. Close and Luigi Cattivelli
Plant Physiology May 2006, Vol. 141, pp. 257–270
PubMed: 16603669
PLEXdb: browse BB65 experiment data

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..
Jain M, Nijhawan A, Arora R, Agarwal P et al.
Plant Physiol 2007 Apr;143(4):1467-83.
PubMed: 17293439
PLEXdb: browse OS5 experiment data

A gene expression map of Arabidopsis thaliana development.
Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Scholkopf B, Weigel D, Lohmann JU
Nat Genet. 2005 May;37(5):501-6. Epub 2005 Apr 3
PubMed: 15806101
PLEXdb: browse AT40 experiment data
browse AT41 experiment data

Microarray Analysis of Late Response to Boron Toxicity in Barley (Hordeum vulgare L.) Leaves.
z MT, Y?lmaz R, Eyido?an F, de Graaff L, Ycel M, ktem HA ? Mehmet Tufan OZ, Remziye YILMAZ, Fusun EYIDOGAN, Leo de GRAAFF, Meral YUCEL, 2, Huseyin Avni OKTEM
Turkish Journal of Agriculture and Forestry, 33: 191-202, 2009.
PLEXdb: browse BB63 experiment data

Blufensin1 negatively impacts Basal defense in response to barley powdery mildew..
Meng Y, Moscou MJ, Wise RP.
Plant Physiol. 2009 Jan;149(1):271-85..
PubMed: 19005086
PLEXdb: browse BB10 experiment data

Evaluation of Target Preparation Methods for Single-Feature Polymorphism Detection in Large Complex Plant Genomes.
Michael Gore,* Peter Bradbury, Ren Hogers, Matias Kirst, Esther Verstege, Jan van Oeveren, Johan Peleman, Edward Buckler, and Michiel van Eijk
The Plant Genome [A Supplement to Crop Science].Crop Sci. 47(S2) S135S148 .July 2007 No. 2.
PubMed: not in pubmed
PLEXdb: browse ZM10 experiment data

A gene expression atlas of the model legume Medicago truncatula.
Vagner Benedito, Ivone Torez-Jerez, Jeremy Murray, Andry Andriankaja, Stacey Allen, Klementina Kakar, Maren Wandrey, Jerome Verdier, Helene Zuber, Thomas Ott, Sandra Moreau, Andreas Niebel, Tancred Frickey, Georg Weiller, Ji He, Xinbin Dai, Patrick Zhao, Yuhong Tang, and Michael Udvardi
The Plant Journal
PubMed: 18410479
PLEXdb: browse ME1 experiment data

Diversification of Lrk/Tak kinase gene clusters is associated with subfunctionalization and cultivar-specific transcript accumulation in barley.
Hu P, Wise RP
2008. Functional & Integrative Genomics
PubMed: 18414912

Transcriptional regulation by a NAC (NAM-ATAF1,2-CUC2) transcription factor attenuates ABA signalling for efficient basal defence towards Blumeria graminis f.sp. hordei in Arabidopsis. .
Jensen MK, Hagedorn PH, de Torres-Zabala M, Grant MR, Rung JH, Collinge DB, Lyngkjaer MF
Plant J. 2008 Aug 6. [Epub ahead of print]
PubMed: 18694460
PLEXdb: browse AT31 experiment data

Transcriptome analysis of high-temperature adult-plant resistance conditioned by Yr39 during the wheatPuccinia striiformis f. sp. tritici interaction .
Tristan E Coram, Matthew L. Settles and Xianming Chen
MOLECULAR PLANT PATHOLOGY (2008) 9(4), 479-493
PubMed: 18705862
PLEXdb: browse TA11 experiment data

Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus.
Tristan E. Coram, Matthew L. Settles, Meinan Wang and Xianming Chen
Theoretical and Applied Genetics. 2008 May 10
PubMed: 18470504

Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots.
Elke Mangelsen, Joachim Kilian, Kenneth W Berendzen, Uner H Kolukisaoglu, Klaus Harter, Christer Jansson and Dierk Wanke
BMC Genomics, 2008, 9:194
PubMed: 18442363

Comparative transcriptome profiling of near-isogenic barley (Hordeum vulgare) lines differing in the allelic state of a major grain protein content locus identifies genes with possible roles in leaf senescence and nitrogen reallocation..
Aravind K. Jukanti, Nancy M. Heidlebaugh, David L. Parrott, Isabelle A. Fischer, Kate McInnerney and Andreas M. Fischer
New Phytologist 177(2):333-349 (Jan 2008).
PubMed: 18028296
PLEXdb: browse BB53 experiment data

Global gene regulation by Fusarium transcription factors Tri6 and Tri10 reveals adaptations for toxin biosynthesis..
Seong, K., Pasquali, M., Song, J., Hilburn, K., McCormick, S., Dong, Y., Xu, J.-R. and Kistler, H.C.
Molecular Microbiology 72: 354-367 (2009).
PubMed: 19320833
PLEXdb: browse FG10 experiment data
browse FG11 experiment data

Parallel expression profiling of barley-stem rust interactions.
Zhang L, Castell-Miller C, Dahl S, Steffenson B, Kleinhofs A.
Funct Integr Genomics. 2008 Jan 15 [Epub ahead of print]..
PubMed: 18196301
PLEXdb: browse BB49 experiment data

Powdery Mildew Induces Defense-Oriented Reprogramming of the Transcriptome in a Susceptible But Not in a Resistant Grapevine.
Raymond W.M. Fung, Martin Gonzalo, Csaba Fekete, Laszlo G. Kovacs, Yan He, Ellen Marsh, Lauren M. McIntyre, Daniel P. Schachtman and Wenping Qiu
Plant Physiol. 2008 Jan;146(1):236-49
PubMed: 17993546
PLEXdb: browse VV12 experiment data
browse VV13 experiment data

Transcript profiling in host-pathogen interactions.
Wise RP, Moscou MJ, Bogdanove AJ, Whitham SA
2007. Annual Review of Phytopathology 45: 329-369.
PubMed: 17480183
PLEXdb: browse BB4 experiment data

Transcriptome analysis of the wheat-Puccinia striiformis f. sp. tritici interaction.
MOLECULAR PLANT PATHOLOGY 9 (2): 157-169 (2008).
PubMed: 18705849
PLEXdb: browse TA9 experiment data

Stress-responsive ATAF1 negatively regulates ABA signalling for efficeint basal defence in Arabidopsis.
Michael K. Jensen, Peter H. Hagedorn, Marta de Torres-Zabala, Murray R. Grant, Jesper H. Rung, David B. Collinge, and Michael F. Lyngkjaer

Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at veraison..
Stefania Pilati, Michele Perazzolli, Andrea Malossini, Alessandro Cestaro, Lorenzo Dematte, Paolo Fontana, Antonio Dal Ri, Roberto Viola, Riccardo Velasco, Claudio Moser.
BMC Genomics 8 (1), 428 (2007).
PubMed: 18034875
PLEXdb: browse VV11 experiment data

The L-type calcium channel, Cch1, affects ascospore discharge and mycelial growth in the filamentous fungus Gibberella zeae (anamorph Fusarium graminearum) .
Hallen HE, Trail F
Eukaryotic Cell 2008 Feb;7(2):415-24
PubMed: 18083828
PLEXdb: browse FG6 experiment data

Transcriptome analysis of trichothecene-induced gene expression in barley..
Boddu J, Cho S, Muehlbauer GJ
Mol Plant Microbe Interact. 2007 Nov;20(11):1364-75
PubMed: 17977148
PLEXdb: browse BB52 experiment data

Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development.
Deluc LG, Grimplet J, Wheatley MD, Tillett RL, Quilici DR, Osborne C, Schooley DA, Schlauch KA, Cushman JC, Cramer GR
BMC Genomics. 2007 Nov 22;8(1):429
PubMed: 18034876
PLEXdb: browse VV5 experiment data

Conidial germination in the filamentous fungus Fusarium graminearum.
Seong KY, Zhao X, Xu JR, Gldener U, Kistler HC
Fungal Genetics and Biology. 2007 Sep 14
PubMed: 17950638
PLEXdb: browse FG7 experiment data

Gene expression quantitative trait locus analysis of 16 000 barley genes reveals a complex pattern of genome-wide transcriptional regulation.
Potokina E, Druka A, Luo Z, Wise R, Waugh R, Kearsey M
The Plant Journal. 2007 Oct 18
PubMed: 17944808
PLEXdb: browse BB21 experiment data

Mapping barley genes to chromosome arms by transcript profiling of wheat-barley ditelosomic chromosome addition lines.
Bilgic, H., Cho, S., Garvin, D.F., and Muehlbauer, G.J.
2007. Genome 50(9):898-906
PubMed: 18059553
PLEXdb: browse BB55 experiment data

Steam-girdling of barley (Hordeum vulgare) leaves leads to carbohydrate accumulation and accelerated leaf senescence, facilitating transcriptomic analysis of senescence-associated genes.
Parrott DL, McInnerney K, Feller U, Fischer AM
2007 New Phytologist 176: 5669
PubMed: 17803641
PLEXdb: browse BB50 experiment data

Mapping translocation breakpoints using a wheat microarray.
Bhat, P.R., Lukaszewski, A , Cui, X., Xu, J., Wanamaker, S., Svensson, JT., Waines, G.,. and Close, TJ.
Nucleic Acids Research (2007) 35 (9):2936-2943.
PubMed: 17439961

A Low Phytic Acid Barley Mutation Alters Seed Gene Expression.
David E. Bowen, Edward J. Souza, Mary J. Guttieri, Victor Raboy, and Jianming Fu
Crop Sci 2007;47 S-149-S-159.
PLEXdb: browse BB22 experiment data

SFP Genotyping From Affymetrix Arrays Is Robust But Largely Detects Cis-acting Expression Regulators.
Z. W. Luo, E. Potokina, A. Druka, R. Wise, R. Waugh and M. J. Kearsey
Genetics, Vol. 176, 789-800, June 2007, Copyright 2007 doi:10.1534/genetics.106.067843
PubMed: 17409081
PLEXdb: browse BB21 experiment data

Distinct biphasic mRNA changes in response to Asian soybean rust infection.
Martijn van de Mortel, Justin C. Recknor, Michelle A. Graham, Dan Nettleton, Jaime D. Dittman, Rex T. Nelson, Cludia V. Godoy, Ricardo V. Abdelnoor, lvaro M.R. Almeida, Thomas J. Baum, Steven A. Whitham
Molecular Plant-Microbe Interactions (2007) Volume 20, Issue 8, pages 887-899. doi:10.1094/MPMI-20-8-0887
PubMed: 17722693
PLEXdb: browse GM2 experiment data

Tissue-specific mRNA expression profiling in grape berry tissues.
Grimplet J, Deluc LG, Tillett RL, Wheatley MD, Schlauch KA, Cramer GR, Cushman JC
BMC Genomics. 2007 Jun 21;8(1):187
PubMed: 17584945
PLEXdb: browse VV3 experiment data

Identifying regions of the wheat genome controlling seed development by mapping expression quantitative trait loci.
Jordan MC, Somers DJ and Banks TW
Plant Biotechnology J. 2007. 5:442-453
PubMed: 17388792

Gene expression associated with compatible viral diseases in grapevine cultivars.
Espinoza C, Vega A, Medina C, Schlauch K, Cramer G, Arce-Johnson P
Funct Integr Genomics 2007 Apr;7(2):95-110. Epub 2006 Jun 15
PubMed: 16775684
PLEXdb: browse VV7 experiment data

Estimating the number of true null hypotheses from a histogram of p-values.
Nettleton D, Hwang JTG, Caldo RA, Wise RP
2006. Journal of Agricultural, Biological, and Environmental Statistics 11: 337-356.
PLEXdb: browse BB4 experiment data

Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles.
Cramer GR, Ergul A, Grimplet J, Tillett RL, Tattersall EA, Bohlman MC, Vincent D, Sonderegger J, Evans J, Osborne C, Quilici D, Schlauch KA, Schooley DA, Cushman JC
Functional & integrative genomics
PubMed: 17136344
PLEXdb: browse VV2 experiment data

Rpr1, a gene required for Rpg1-dependent resistance to stem rust in barley.
Zhang L, Fetch T, Nirmala1 J, Schmierer D, Brueggeman R, Steffenson B, Kleinhofs A
TAG Theoretical and Applied Genetics. Volume 113, Number 5 / September, 2006
PubMed: 16832646
PLEXdb: browse BB28 experiment data

Stage-specific suppression of basal defense discriminates barley plants containing fast- and delayed-acting Mla powdery mildew resistance alleles.
Caldo RA, Nettleton D, Peng J, Wise RP
Molecular Plant-Microbe Interactions. 2006 Sep;19(9):939-47
PubMed: 16941898
PLEXdb: browse BB2 experiment data
browse BB4 experiment data

Genetic diversity contribution to errors in short oligonucleotide microarray analysis.
Kirst M, Caldo R, Casati P, Tanimoto G, Walbot V, Wise RP,5 and Buckler ES
Plant Biotechnology Journal. Online Early. doi:10.1111/j.1467-7652.2006.00198.x.

Transcriptome Analysis of Cold Acclimation in Barley Albina and Xantha Mutants.
Svensson JT, Crosatti C, Campoli C, Bassi R, Stanca AM, Close TJ, Cattivelli L
Plant Physiology 2006 May;141(1):257-70. Epub 2006 Apr 7.
PubMed: 16603669

Transcriptome Analysis of the Barley - Fusarium graminearum Interaction.
Boddu J, Cho S, Kruger WM, and Muehlbauer GJ
Molecular Plant-Microbe Interactions. 2006 April;19(4):407-417.
PubMed: 16610744
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An atlas of gene expression from seed to seed through barley development.
Druka A, Muehlbauer G, Druka I, Caldo R, Baumann U, Rostoks N, Schreiber A, Wise R, Close T, Kleinhofs A, Graner A, Schulman A, Langridge P, Sato K, Hayes P, McNicol J, Marshall D, Waugh R
Functional & Integrative Genomics. 2006 Mar
PubMed: 16547597
PLEXdb: browse BB3 experiment data

Development of a Fusarium graminearum Affymetrix GeneChip for profiling fungal gene expression in vitro and in planta.
Guldener U, Seong KY, Boddu J, Cho S, Trail F, Xu JR, Adam G, Mewes HW, Muehlbauer GJ, Kistler HC
Fungal Genetics and Biology. 2006 Mar 10
PubMed: 16531083
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Genetic Regulation of Gene Expression During Shoot Development in Arabidopsis.
DeCook R, Lall S, Nettleton D and Howell SH
Genetics. 2006 Feb;172(2):1155-1164.
PubMed: 15956669
PLEXdb: browse AT10 experiment data

Transcriptome analysis and physical mapping of barley genes in wheat-barley chromosome addition lines.
Cho S, Garvin DF, Muehlbauer GJ
Genetics. 2006 Feb;172(2):1277-85.
PubMed: 16322516
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Expression analysis of barley (Hordeum vulgare L.) during salinity stress.
Walia H, Wilson C, Wahid A, Condamine P, Cui X, Close TJ
Functional & Integrative Genomics. 2006 Mar;6(2):143-156
PubMed: 16450154

Comparative Transcriptional Profiling of Two Contrasting Rice Genotypes under salinity stress during the vegetative growth stage.
Walia H, Wilson C, Condamine P, Liu X, Ismail AM, Zeng L, Wanamaker SI, Mandal J, Xu J, Cui X, Close TJ
2005 Oct;139(2):822-35. Epub 2005 Sep 23
PubMed: 16183841

A comparative analysis of transcript abundance using SAGE and Affymetrix arrays.
Ibrahim AF, Hedley PE, Cardle L, Kruger W, Marshall DF, Muehlbauer GJ, Waugh R
Functional & Integrative Genomics. 2005 Jul;5(3):163-74.
PubMed: 15714318

Detecting single-feature polymorphisms using oligonucleotide arrays and robustified projection pursuit.
Cui X, Xu J, Asghar R, Condamine P, Svensson JT, Wanamaker S, Stein N, Roose M, and Close TJ
Bioinformatics Advance Access published online on August 23, 2005.
PubMed: 16118260

Single-feature polymorphism discovery in the barley transcriptome.
Rostoks N, Borevitz JO, Hedley PE, Russell J, Mudie S, Morris J, Cardle L, Marshall DF, Waugh R
Genome Biology. 2005, June;6(6).
PubMed: 15960806
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Transcriptome profiling of the response of Arabidopsis thaliana suspension culture cells to sucrose starvation.
Contento AL, Kim SJ and Bassham DC
Plant Physiology, 135(4), 2330-47.
PubMed: 15310832
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Interaction-Dependent Gene Expression in Mla-Specified Response to Barley Powdery Mildew.
Rico A. Caldo, Dan Nettleton and Roger P. Wise
Plant Cell. 16:2514-2528 (2004).
PubMed: 15319481
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Cutting Edge Transcriptome Analysis: It's All about Design.
Nancy A. Eckardt, News and Reviews Editor
Plant Cell. 16:2249-2251 (2004).

A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning.
Mitra RM, Gleason CA, Edwards A, Hadfield J, Downie JA, Oldroyd GE, Long SR
Proc Natl Acad Sci U S A. 2004 Mar 30;101(13):4701-5
PubMed: 15070781
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A New Resource for Cereal Genomics: 22K Barley GeneChip Comes of Age.
Close TJ, Wanamaker SI, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP
Plant Physiol. 2004 Mar;134(3):960-8.
PubMed: 15020760
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