We are analyzing https://link.springer.com/article/10.1186/gb-2008-9-8-r130.

Title:
Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development | Genome Biology
Description:
Background As nonmotile organisms, plants must rapidly adapt to ever-changing environmental conditions, including those caused by daily light/dark cycles. One important mechanism for anticipating and preparing for such predictable changes is the circadian clock. Nearly all organisms have circadian oscillators that, when they are in phase with the Earth
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Keywords {🔍}

genes, circadian, pubmed, article, google, scholar, cas, clock, plant, figure, datasets, covington, transcript, regulation, expression, arabidopsis, regulated, central, data, time, gene, edwards, circadianregulated, found, analysis, microarray, pathways, dataset, abundance, phase, expressed, subjective, aba, shown, ethylene, clockregulated, atg, harmer, plants, levels, acid, physiol, identified, stress, genome, michael, promoters, accumulation, cell, responses,

Topics {✒️}

multiple-measures-corrected significance probability 1-deoxy-d-xylulose-5-phosphate synthase myb protein early-phytochrome-responsive1 day-specific cis-regulatory modules article download pdf teosinte branched1/cycloidia/pcf article number r130 myb-related transcription factor circadian-regulated hormone-responsive genes estimated experiment-wise critical brassinosteroid-biosynthetic cpd gene cadpr-based feedback loop confers midnight-phased expression circadian-regulated heat-induced genes confers dawn-phased expression full size image day-specific circadian expression post-transcriptional mechanisms show phase-specific enrichment clock-regulated carotenoid genes medium-sized colored arrows dchip-derived standard error circadian-regulated genes responsive acc-repressed genes tend heat-responsive genes peaks late day-phased motif detecting clock-regulated genes similar day-phased pattern dawn-phased transcript accumulation phase-specific transcript accumulation national research initiative methyl erythritol phosphate control phase-specific expression daily light/dark cycles clock-regulated transcript abundance g-protein-mediated signaling reactive oxygen species confer dawn-phased rhythms scripps research institute daily light-dark cycle authors’ original file slave circadian oscillator fewer circadian-regulated genes clock-regulated transcript accumulation clustered clock-regulated genes privacy choices/manage cookies phase-specific ccre present clock-regulated tcp genes cis-regulatory elements rate-limiting enzymes cla1

Questions {❓}

Therefore, the question remains, how is the observed diverse array of circadian phases of transcript abundance generated?

Schema {🗺️}

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         description:As nonmotile organisms, plants must rapidly adapt to ever-changing environmental conditions, including those caused by daily light/dark cycles. One important mechanism for anticipating and preparing for such predictable changes is the circadian clock. Nearly all organisms have circadian oscillators that, when they are in phase with the Earth's rotation, provide a competitive advantage. In order to understand how circadian clocks benefit plants, it is necessary to identify the pathways and processes that are clock controlled. We have integrated information from multiple circadian microarray experiments performed on Arabidopsis thaliana in order to better estimate the fraction of the plant transcriptome that is circadian regulated. Analyzing the promoters of clock-controlled genes, we identified circadian clock regulatory elements correlated with phase-specific transcript accumulation. We have also identified several physiological pathways enriched for clock-regulated changes in transcript abundance, suggesting they may be modulated by the circadian clock. Our analysis suggests that transcript abundance of roughly one-third of expressed A. thaliana genes is circadian regulated. We found four promoter elements, enriched in the promoters of genes with four discrete phases, which may contribute to the time-of-day specific changes in the transcript abundance of these genes. Clock-regulated genes are over-represented among all of the classical plant hormone and multiple stress response pathways, suggesting that all of these pathways are influenced by the circadian clock. Further exploration of the links between the clock and these pathways will lead to a better understanding of how the circadian clock affects plant growth and leads to improved fitness.
         datePublished:2008-08-18T00:00:00Z
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         Animal Genetics and Genomics
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         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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      name:Center for Biomathematical Technology, University of Virginia Health Sciences System, Charlottesville, USA
      name:Customized Online Biomathematical Research Applications, Glenaire Drive, Charlottesville, USA
      name:Department of Biochemistry, The Scripps Research Institute, La Jolla, USA
      name:Section of Cell and Developmental Biology, University of California at San Diego, Gilman Drive, La Jolla, USA
      name:Department of Plant Biology, College of Biological Sciences, One Shields Avenue, University of California, Davis, USA

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