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Kenneth Birnbaum,1Dennis E. Shasha,2Jean Y. Wang,3Jee W. Jung,1Georgina M. Lambert,4David W. Galbraith,4Philip N. Benfey3*
A global map of gene expression within an organ can identifygenes with coordinated expression in localized domains, therebyrelating gene activity to cell fate and tissue specialization.Here, we present localization of expression of more than 22,000genes in the Arabidopsis root. Gene expression was mapped to15 different zones of the root that correspond to cell typesand tissues at progressive developmental stages. Patterns ofgene expression traverse traditional anatomical boundaries andshow cassettes of hormonal response. Chromosomal clusteringdefined some coregulated genes. This expression map correlatesgroups of genes to specific cell fates and should serve to guidereverse genetics.
1 Department of Biology, New York University, New York, NY 10003, USA. 2 Courant Institute of Mathematical Sciences, New York University, New York, NY 10003, USA. 3 Department of Biology, Duke University, Box 91000, Durham, NC 27708, USA. 4 Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
* To whom correspondence should be addressed. E-mail: philip.benfey{at}duke.edu
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PNAS
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Plant Physiology
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148, 796-807
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135, 2573-2582
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20, 2102-2116
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Plant Physiology
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PNAS
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Plant Physiology
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318, 801-806
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Plant Physiology
145, 575-588
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Plant Physiology
145, 843-852
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PNAS
104, 15572-15577
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Plant Physiology
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PLANT CELL
19, 1838-1850
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From the Cover: A gene essential for hydrotropism in roots.
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PNAS
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134, 681-690
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Plant Physiology
143, 924-940
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PLANT CELL
19, 131-147
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F. Beisson, Y. Li, G. Bonaventure, M. Pollard, and J. B. Ohlrogge (2007)
PLANT CELL
19, 351-368
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PNAS
103, 19206-19211
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D. Van Damme, S. Coutuer, R. De Rycke, F.-Y. Bouget, D. Inze, and D. Geelen (2006)
PLANT CELL
18, 3502-3518
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PLANT CELL
18, 3145-3157
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CER4 Encodes an Alcohol-Forming Fatty Acyl-Coenzyme A Reductase Involved in Cuticular Wax Production in Arabidopsis.
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Plant Physiology
142, 866-877
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Unraveling the dynamic transcriptome..
S. M. Brady, T. A. Long, and P. N. Benfey (2006)
PLANT CELL
18, 2101-2111
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The CLAVATA3/ESR Motif of CLAVATA3 Is Functionally Independent from the Nonconserved Flanking Sequences.
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Plant Physiology
141, 1284-1292
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57, 2401-2411
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PNAS
103, 9738-9743
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Expression Profiling of Auxin-treated Arabidopsis Roots: Toward a Molecular Analysis of Lateral Root Emergence.
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47, 788-792
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SCARFACE Encodes an ARF-GAP That Is Required for Normal Auxin Efflux and Vein Patterning in Arabidopsis.
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PLANT CELL
18, 1396-1411
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LucTrap Vectors Are Tools to Generate Luciferase Fusions for the Quantification of Transcript and Protein Abundance in Vivo..
L. I. A. Calderon-Villalobos, C. Kuhnle, H. Li, M. Rosso, B. Weisshaar, and C. Schwechheimer (2006)
Plant Physiology
141, 3-14
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103, 6055-6060
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Arabidopsis TEBICHI, with Helicase and DNA Polymerase Domains, Is Required for Regulated Cell Division and Differentiation in Meristems.
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PLANT CELL
18, 879-892
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M. S. Pischke, E. L. Huttlin, A. D. Hegeman, and M. R. Sussman (2006)
Plant Physiology
140, 1255-1278
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Progressive Inhibition by Water Deficit of Cell Wall Extensibility and Growth along the Elongation Zone of Maize Roots Is Related to Increased Lignin Metabolism and Progressive Stelar Accumulation of Wall Phenolics.
L. Fan, R. Linker, S. Gepstein, E. Tanimoto, R. Yamamoto, and P. M. Neumann (2006)
Plant Physiology
140, 603-612
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The Arabidopsis genome: A foundation for plant research.
Functional Genomic Analysis of the AUXIN/INDOLE-3-ACETIC ACID Gene Family Members in Arabidopsis thaliana.
P. J. Overvoorde, Y. Okushima, J. M. Alonso, A. Chan, C. Chang, J. R. Ecker, B. Hughes, A. Liu, C. Onodera, H. Quach, et al. (2005)
PLANT CELL
17, 3282-3300
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Cuticular Lipid Composition, Surface Structure, and Gene Expression in Arabidopsis Stem Epidermis.
M. C. Suh, A. L. Samuels, R. Jetter, L. Kunst, M. Pollard, J. Ohlrogge, and F. Beisson (2005)
Plant Physiology
139, 1649-1665
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Multiple Type-B Response Regulators Mediate Cytokinin Signal Transduction in Arabidopsis.
M. G. Mason, D. E. Mathews, D. A. Argyros, B. B. Maxwell, J. J. Kieber, J. M. Alonso, J. R. Ecker, and G. E. Schaller (2005)
PLANT CELL
17, 3007-3018
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Isolation, Characterization, and Pericycle-Specific Transcriptome Analyses of the Novel Maize Lateral and Seminal Root Initiation Mutant rum1.
K. Woll, L. A. Borsuk, H. Stransky, D. Nettleton, P. S. Schnable, and F. Hochholdinger (2005)
Plant Physiology
139, 1255-1267
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Histone acetylation affects expression of cellular patterning genes in the Arabidopsis root epidermis.
C.-R. Xu, C. Liu, Y.-L. Wang, L.-C. Li, W.-Q. Chen, Z.-H. Xu, and S.-N. Bai (2005)
PNAS
102, 14469-14474
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A microarray analysis of the rice transcriptome and its comparison to Arabidopsis.
L. Ma, C. Chen, X. Liu, Y. Jiao, N. Su, L. Li, X. Wang, M. Cao, N. Sun, X. Zhang, et al. (2005)
Genome Res.
15, 1274-1283
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GAL4-GFP enhancer trap lines for genetic manipulation of lateral root development in Arabidopsis thaliana.
L. Laplaze, B. Parizot, A. Baker, L. Ricaud, A. Martiniere, F. Auguy, C. Franche, L. Nussaume, D. Bogusz, and J. Haseloff (2005)
J. Exp. Bot.
56, 2433-2442
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The small GTPase AtRAC2/ROP7 is specifically expressed during late stages of xylem differentiation in Arabidopsis.
