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PLEXdb is committed to making
microarray data publicly available to researchers world-wide...
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Publications
How to cite
PLEXdb
About BarleyBase/PLEXdb |
Cite or use BarleyBase/PLEXdb
Publications about BarleyBase/PLEXdb
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BarleyBase/PLEXdb: A Unified Expression Profiling Database for
Plants and Plant Pathogens
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Wise RP, Caldo RA, Hong L, Shen L, Cannon EK, Dickerson JA.
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Pages 347-363 In Methods in Molecular Biology, Vol. 406, Plant
Bioinformatics - Methods and Protocols. Edwards D. ed. Humana Press,
Totowa, NJ. 2007.
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Please cite PLEXdb using this paper if your publication uses
tools or data from PLEXdb.
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- BarleyBase An expression profiling
database for plant genomics
- Lishuang Shen, Jian Gong, Rico A. Caldo, Dan Nettleton, Dianne Cook,
Roger P. Wise and Julie A. Dickerson
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Nucleic Acids Research, 2005, Vol. 33, Database issue D614-D618
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PubMed:
15608273
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BarleyExpress: a web-based
submission tool for enriched microarray database annotations
- Tang X, Shen L, Dickerson JA.
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Bioinformatics 2005 21(3):399-401
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PubMed:
15347571
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Publications which cite or use BarleyBase/PLEXdb
- 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
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- 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
- PLEXdb: browse TA9 experiment data
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- 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
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- Global Gene Regulation by Fusarium Transcription Factors Tri6 and Tri10 Reveals Adaptations for Toxin Biosynthesis..
- Kye-Yong Seong, Matias Pasquali, Jongwoo Song, Karen Hilburn, Susan McCormick, Yanhong Dong, Jin-Rong Xu, and H. Corby Kistler
- PLoS Pathogens
- PLEXdb:
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- 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
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- 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. 146: 236-249
- PubMed: 17993546
- PLEXdb: browse VV12 experiment data
browse VV13 experiment data
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- 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
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- Transcriptome analysis of the wheat–Puccinia striiformis f. sp. tritici interaction.
- TRISTAN E. CORAM, MEINAN WANG AND XIANMING CHEN
- MOLECULAR PLANT PATHOLOGY 9 (2): 157-169 (2008).
- PLEXdb: browse TA9 experiment data
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- 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
- PLEXdb:
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- 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
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- The L-type calcium channel, Cch1, affects ascospore discharge and mycelial growth in the filamentous fungus Gibberella zeae (anamorph Fusarium graminearum)
[published ahead of print on 14
December 2007, doi:10.1128/EC.00248-07].
- Hallen HE, F
Trail
- Eukaryotic Cell
- PLEXdb: browse FG6 experiment data
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- 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
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- 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
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- Conidial germination in the filamentous fungus Fusarium graminearum.
- Seong KY, Zhao X, Xu JR, Güldener U, Kistler HC
- Fungal Genetics and Biology. 2007 Sep 14
- PubMed: 17950638
- PLEXdb: browse FG7 experiment data
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- 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:
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- 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
- PLEXdb: browse BB55 experiment data
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- 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: 56–69
- PubMed: 17803641
- PLEXdb: browse BB50 experiment data
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- 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, 35 (9):2936-2943.
- PubMed: 17439961
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- 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
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- 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:
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- 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, Cláudia V. Godoy, Ricardo V. Abdelnoor,
Álvaro 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
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- 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
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- 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
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- 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
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- 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
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- 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
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- 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
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- 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
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- 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.
- PLEXdb: browse ZM1 experiment data
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- 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
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- 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
- PLEXdb: browse BB9 experiment data
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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
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- 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
- PLEXdb: browse FG1 experiment data
browse FG2 experiment data
browse FG3 experiment data
browse FG4 experiment data
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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
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- 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
- PLEXdb: browse BB8 experiment data
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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
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- 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
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- 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
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- 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
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- 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
- PLEXdb: browse BB3 experiment data
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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
- PLEXdb: browse AT8 experiment data
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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
- PLEXdb: browse BB4 experiment data
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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).
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- 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
- PLEXdb: browse BB5 experiment data
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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
- PLEXdb: browse BB1 experiment data
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