Title Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis Suggested running title : Transcriptional Landscape of Arabidopsis

This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as an 'Accepted Article', doi: 10.1111/tpj.13175 This article is protected by copyright. All rights reserved. Received Date : 16-Oct-2015 Accepted Date : 21-Mar-2016 Article type : Original Article

[1]  Subhajyoti De,et al.  An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples , 2015, Briefings Bioinform..

[2]  Ben Lehner,et al.  The effects of genetic variation on gene expression dynamics during development , 2013, Nature.

[3]  John Ralph,et al.  Caffeoyl Shikimate Esterase (CSE) Is an Enzyme in the Lignin Biosynthetic Pathway in Arabidopsis , 2013, Science.

[4]  Ellen T. Gelfand,et al.  The Genotype-Tissue Expression (GTEx) project , 2013, Nature Genetics.

[5]  Xing Qiu,et al.  The impact of quantile and rank normalization procedures on the testing power of gene differential expression analysis , 2013, BMC Bioinformatics.

[6]  A. Brazma,et al.  Reuse of public genome-wide gene expression data , 2012, Nature Reviews Genetics.

[7]  Barry Smith,et al.  The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses , 2012, Plant & cell physiology.

[8]  Barry Smith,et al.  Ontologies as Integrative Tools for Plant Science Nih Public Access Author Manuscript $watermark-text Ontology 101 $watermark-text , 2022 .

[9]  H. Parkinson,et al.  Large scale comparison of global gene expression patterns in human and mouse , 2010, Genome Biology.

[10]  Robert Turgeon,et al.  The developmental dynamics of the maize leaf transcriptome , 2010, Nature Genetics.

[11]  H. Parkinson,et al.  A global map of human gene expression , 2010, Nature Biotechnology.

[12]  Li Liu,et al.  A dynamic gene expression atlas covering the entire life cycle of rice. , 2010, The Plant journal : for cell and molecular biology.

[13]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[14]  Staffan Persson,et al.  GeneCAT—novel webtools that combine BLAST and co-expression analyses , 2008, Nucleic Acids Res..

[15]  Kenneth D. Birnbaum,et al.  Slicing across Kingdoms: Regeneration in Plants and Animals , 2008, Cell.

[16]  Kazuki Saito,et al.  Identification of a Flavonol 7-O-Rhamnosyltransferase Gene Determining Flavonoid Pattern in Arabidopsis by Transcriptome Coexpression Analysis and Reverse Genetics*♦ , 2007, Journal of Biological Chemistry.

[17]  Paul A Clemons,et al.  The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease , 2006, Science.

[18]  Kiana Toufighi,et al.  The Botany Array Resource: E-northerns, Expression Angling, and Promoter Analyses , 2022 .

[19]  Stefan R. Henz,et al.  A gene expression map of Arabidopsis thaliana development , 2005, Nature Genetics.

[20]  Dennis B. Troup,et al.  NCBI GEO: mining millions of expression profiles—database and tools , 2004, Nucleic Acids Res..

[21]  P. Zimmermann,et al.  GENEVESTIGATOR. Arabidopsis Microarray Database and Analysis Toolbox1[w] , 2004, Plant Physiology.

[22]  Wei-Min Liu,et al.  Robust estimators for expression analysis , 2002, Bioinform..

[23]  G. Churchill Fundamentals of experimental design for cDNA microarrays , 2002, Nature Genetics.

[24]  A. Schulze,et al.  Navigating gene expression using microarrays — a technology review , 2001, Nature Cell Biology.

[25]  홀덴 데이비드윌리암,et al.  Identification of genes , 1995 .

[26]  M. Timko,et al.  Leaf Developmental Age Controls Expression of Genes Encoding Enzymes of Chlorophyll and Heme Biosynthesis in Pea (Pisum sativum L.) , 1994, Plant physiology.

[27]  J. Ludlow,et al.  Organ Regeneration , 2013, Methods in Molecular Biology.

[28]  Lei Guo,et al.  The MicroArray Quality Control (MAQC) Project and Cross-Platform Analysis of Microarray Data , 2011, Handbook of Statistical Bioinformatics.

[29]  Dennis Shasha,et al.  VirtualPlant: A Software Platform to Support Systems , 2010 .