Journal ArticleDOI
A gene expression map of Arabidopsis thaliana development
Markus Schmid,Timothy S. Davison,Stefan R. Henz,Utz Johann Pape,Monika Demar,Martin Vingron,Bernhard Schölkopf,Detlef Weigel,Detlef Weigel,Jan U. Lohmann +9 more
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TLDR
Examining the expression patterns of large gene families, it is found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.Abstract:
Regulatory regions of plant genes tend to be more compact than those of animal genes, but the complement of transcription factors encoded in plant genomes is as large or larger than that found in those of animals. Plants therefore provide an opportunity to study how transcriptional programs control multicellular development. We analyzed global gene expression during development of the reference plant Arabidopsis thaliana in samples covering many stages, from embryogenesis to senescence, and diverse organs. Here, we provide a first analysis of this data set, which is part of the AtGenExpress expression atlas. We observed that the expression levels of transcription factor genes and signal transduction components are similar to those of metabolic genes. Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.read more
Citations
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Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis
TL;DR: Hundreds of Arabidopsis genes were found that outperform traditional reference genes in terms of expression stability throughout development and under a range of environmental conditions, and the developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels inArabidopsis in the future.
Journal ArticleDOI
An “Electronic Fluorescent Pictograph” Browser for Exploring and Analyzing Large-Scale Biological Data Sets
TL;DR: The eFP Browser software is easily adaptable to microarray or other large-scale data sets from any organism and thus should prove useful to a wide community for visualizing and interpreting these data sets for hypothesis generation.
Journal ArticleDOI
Abscisic Acid Inhibits Type 2C Protein Phosphatases via the PYR/PYL Family of START Proteins
Sang-Youl Park,Pauline Fung,Noriyuki Nishimura,Davin R. Jensen,Hiroaki Fujii,Yang Zhao,Shelley Lumba,Julia Santiago,Americo Rodrigues,Tsz-fung Freeman Chow,Simon E. Alfred,Dario Bonetta,Ruth R. Finkelstein,Nicholas J. Provart,Darrell Desveaux,Pedro L. Rodriguez,Peter McCourt,Jian-Kang Zhu,Julian I. Schroeder,Brian F. Volkman,Sean R. Cutler +20 more
TL;DR: PYR/PYLs are ABA receptors functioning at the apex of a negative regulatory pathway that controls ABA signaling by inhibiting PP2Cs, illustrating the power of the chemical genetic approach for sidestepping genetic redundancy.
Journal ArticleDOI
Gene networks involved in drought stress response and tolerance
TL;DR: In this paper, a short review of recent progress resulting from analysis of gene expression during the drought-stress response in plants as well as in elucidating the functions of genes implicated in the stress response and/or stress tolerance are summarized.
Journal ArticleDOI
JAZ repressor proteins are targets of the SCF COI1 complex during jasmonate signalling
Bryan Thines,Leron Katsir,Maeli Melotto,Yajie Niu,Ajin Mandaokar,Guanghui Liu,Kinya Nomura,Sheng Yang He,Gregg A. Howe,John Browse +9 more
TL;DR: The results suggest a model in which jasmonate ligands promote the binding of the SCFCOI1 ubiquitin ligase to and subsequent degradation of the JAZ1 repressor protein, and implicate theSCFCOi1–JAZ1 protein complex as a site of perception of the plant hormone JA–Ile.
References
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Journal ArticleDOI
Cluster analysis and display of genome-wide expression patterns
TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
Journal ArticleDOI
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
TL;DR: This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.
Journal ArticleDOI
Nonlinear component analysis as a kernel eigenvalue problem
TL;DR: A new method for performing a nonlinear form of principal component analysis by the use of integral operator kernel functions is proposed and experimental results on polynomial feature extraction for pattern recognition are presented.
Journal Article
Preservation of duplicate genes by complementary, degenerative mutations.
TL;DR: Cooke et al. as mentioned in this paper proposed a new conceptual framework for understanding the evolution of duplicate genes that may help explain this conundrum, focusing on the regulatory complexity of eukaryotic genes, and showed how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the development of new gene functions.
Journal ArticleDOI
Preservation of Duplicate Genes by Complementary, Degenerative Mutations
TL;DR: Focusing on the regulatory complexity of eukaryotic genes, it is shown how complementary degenerative mutations in different regulatory elements of duplicated genes can facilitate the preservation of both duplicates, thereby increasing long-term opportunities for the evolution of new gene functions.
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