Publications
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About BarleyBase/PLEXdb | Cite or use BarleyBase/PLEXdb

Publications about BarleyBase/PLEXdb

BarleyBase/PLEXdb: A Unified Expression Profiling Database for Plants and Plant Pathogens

Wise RP, Caldo RA, Hong L, Shen L, Cannon EK, Dickerson JA.

Pages 347-363 In Methods in Molecular Biology, Vol. 406, Plant Bioinformatics - Methods and Protocols. Edwards D. ed. Humana Press, Totowa, NJ. 2007.

Please cite PLEXdb using this paper if your publication uses tools or data from PLEXdb.

 

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

Nucleic Acids Research, 2005, Vol. 33, Database issue D614-D618

PubMed: 15608273

 

BarleyExpress: a web-based submission tool for enriched microarray database annotations

Tang X, Shen L, Dickerson JA.

Bioinformatics 2005 21(3):399-401

PubMed: 15347571

 

 

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

 

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

 

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..

Kye-Yong Seong, Matias Pasquali, Jongwoo Song, Karen Hilburn, Susan McCormick, Yanhong Dong, Jin-Rong Xu, and H. Corby Kistler

PLoS Pathogens

PLEXdb:

 

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. 146: 236-249

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.

TRISTAN E. CORAM, MEINAN WANG AND XIANMING CHEN

MOLECULAR PLANT PATHOLOGY 9 (2): 157-169 (2008).

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

PLEXdb:

 

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) [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

 

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, Güldener 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:

 

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

 

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

 

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

 

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:

 

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

 

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.

PLEXdb: browse ZM1 experiment data

 

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

PLEXdb: browse BB9 experiment data

 

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

PLEXdb: browse FG1 experiment data
browse FG2 experiment data
browse FG3 experiment data
browse FG4 experiment data

 

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

PLEXdb: browse BB8 experiment data

 

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

PLEXdb: browse BB3 experiment data

 

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

 

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

 

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

PLEXdb: browse BB5 experiment data

 

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