Genome-Wide Patterns of Arabidopsis Gene Expression in Nature
Publication Date
April 19, 2012
Journal
PLOS Genetics
Authors
Christina L. Richards, Ulises Rosas, Joshua Banta, Naeha Bhambhra, et al
Volume
8
Issue
4
Pages
e1002662
DOI
https://dx.plos.org/10.1371/journal.pgen.1002662
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1002662
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22532807
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3330097
Europe PMC
http://europepmc.org/abstract/MED/22532807
Web of Science
000303441800037
Scopus
84860567710
Mendeley
http://www.mendeley.com/research/genomewide-patterns-arabidopsis-gene-expression-nature
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Mendeley | Further Information

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CrossRef

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/650231"], "description"=>"<p>(A) The top graph shows the daily maximum (red) and minimum temperatures (blue), and the lower graph shows the daily levels of precipitation in the field during the experiment. The sampling days (given as days after germination) are shown in the bottom. The arrows indicate the sampling points, and the onset of flowering for Bay-0 and Sha in the experiment are shown. (B) The total number of genes expressed in Bay-0 and Sha in the field, compared to those observed for Col-0 shoot tissue in the ATGenExpress data set <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002662#pgen.1002662-Schmid1\" target=\"_blank\">[29]</a>.</p>", "links"=>[], "tags"=>["conditions"], "article_id"=>320720, "categories"=>["Ecology", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Christina L. Richards", "Ulises Rosas", "Joshua Banta", "Naeha Bhambhra", "Michael D. Purugganan"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002662.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Field_environmental_conditions_and_total_gene_expression_in_A_thaliana_/320720", "title"=>"Field environmental conditions and total gene expression in <i>A. thaliana</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-19 00:12:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/650318"], "description"=>"<p>The numbers listed to the left indicate the cluster number identified in the silhouette analyses. The four most significant (i.e., lowest <i>p</i> values) GO term categories enriched for each cluster are shown on the left. The vegetative and flowering samples are indicated at the top, and the rows corresponding to various flower development genes are shown. Several developmental genes associated with bolting and flower development are highlighted. Scale: from brightest blue equals most down-regulated to brightest red equals most up-regulated.</p>", "links"=>[], "tags"=>["bay-0", "genes", "differential"], "article_id"=>320804, "categories"=>["Ecology", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Christina L. Richards", "Ulises Rosas", "Joshua Banta", "Naeha Bhambhra", "Michael D. Purugganan"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002662.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heat_map_for_Bay_0_genes_that_show_differential_expression_during_flowering_/320804", "title"=>"Heat map for Bay-0 genes that show differential expression during flowering.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-19 00:13:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/650390"], "description"=>"<p>(A) The number of genes that significantly differ between Bay and Sha accessions, flowering status, and that show an accession-by-flowering status (development) interaction. (B) The percent of the transcriptional variance explained by these factors.</p>", "links"=>[], "tags"=>["transcriptional", "variance"], "article_id"=>320885, "categories"=>["Ecology", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Christina L. Richards", "Ulises Rosas", "Joshua Banta", "Naeha Bhambhra", "Michael D. Purugganan"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002662.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Components_of_transcriptional_variance_in_A_thaliana_in_the_field_/320885", "title"=>"Components of transcriptional variance in <i>A. thaliana</i> in the field.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-19 00:14:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/650467"], "description"=>"<p>The blue indicates Bay-0 and the red Sha.</p>", "links"=>[], "tags"=>["components", "transcriptional", "variance"], "article_id"=>320952, "categories"=>["Ecology", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Christina L. Richards", "Ulises Rosas", "Joshua Banta", "Naeha Bhambhra", "Michael D. Purugganan"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002662.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Environmental_components_of_transcriptional_variance_in_A_thaliana_in_the_field_/320952", "title"=>"Environmental components of transcriptional variance in <i>A. thaliana</i> in the field.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-19 00:15:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/650524"], "description"=>"<p>Silhouette analysis defined (A) 188 clusters in Sha and (B) 109 clusters in Bay-0. Each row indicates a specific cluster. The components of the transcriptional variance explained by environmental (precipitation, maximum and minimum daily temperatures) and developmental factors (age and flowering status) are shown. The percent of the transcriptional variance explained by a factor is shown in color (blue, <25%; yellow, between 25–50%; orange, between 50–75%; red, >75%). We also examined each cluster for enrichment of genes shown to be differentially expressed in previously-studied transcriptome analyses. A red bar indicates that the cluster is enriched in genes differentially expressed under that stress condition.</p>", "links"=>[], "tags"=>["clusters"], "article_id"=>321017, "categories"=>["Ecology", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Christina L. Richards", "Ulises Rosas", "Joshua Banta", "Naeha Bhambhra", "Michael D. Purugganan"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002662.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expression_clusters_in_A_thaliana_field_transcriptomes_/321017", "title"=>"Gene expression clusters in <i>A. thaliana</i> field transcriptomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-19 00:16:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/650648"], "description"=>"<p>The first five principal components are indicated. Principal component scores are on the y-axis and sampling days on the x-axis. The dashed line gives the PC score for Bay-0 and the dotted line for Sha. At each sampling day, the mean PC score across the three replicates are given for Bay-0 (circles) and Sha (squares), with standard error bars (+/− 1 SE).</p>", "links"=>[], "tags"=>["analyses"], "article_id"=>321140, "categories"=>["Ecology", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Christina L. Richards", "Ulises Rosas", "Joshua Banta", "Naeha Bhambhra", "Michael D. Purugganan"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002662.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Vegetative_stage_principal_component_analyses_of_A_thaliana_field_transcriptome_/321140", "title"=>"Vegetative stage principal component analyses of <i>A. thaliana</i> field transcriptome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-19 00:19:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/650708"], "description"=>"<p>Each point is the LS mean expression level of (A) <i>ARP6</i> and (B) <i>HSP70</i> in Bay-0 (open circles) and Sha (closed circles) for each time point. The dashed line shows the linear regression through the data. *** = p<0.001.</p>", "links"=>[], "tags"=>["conditions", "correlated"], "article_id"=>321197, "categories"=>["Ecology", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Christina L. Richards", "Ulises Rosas", "Joshua Banta", "Naeha Bhambhra", "Michael D. Purugganan"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002662.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expression_in_A_thaliana_under_field_conditions_correlated_with_PC1_veg_/321197", "title"=>"Gene expression in <i>A. thaliana</i> under field conditions correlated with PC1<sup>veg</sup>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-19 00:19:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/650791"], "description"=>"<p>Each point is the LS mean expression level of (A) <i>ROP10</i> and (B) <i>AAO3</i> in Bay-0 (open circles) and Sha (closed circles) for each timepoint. The dashed line shows the linear regression through the data. *** = p<0.001.</p>", "links"=>[], "tags"=>["conditions", "correlated"], "article_id"=>321281, "categories"=>["Ecology", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Christina L. Richards", "Ulises Rosas", "Joshua Banta", "Naeha Bhambhra", "Michael D. Purugganan"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002662.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expression_in_A_thaliana_under_field_conditions_correlated_with_PC2_veg_/321281", "title"=>"Gene expression in <i>A. thaliana</i> under field conditions correlated with PC2<sup>veg</sup>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-04-19 00:21:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/650832"], "description"=>"<p>TMAX: Maximum daily temperature, PPT: daily precipitation; RLN: rosette leaf number.</p>***<p>p<0.001;</p>**<p>p<0.01.</p>*<p>p<0.05.</p>", "links"=>[], "tags"=>["vegetative", "components", "genome-wide"], "article_id"=>321327, "categories"=>["Ecology", "Genetics", "Plant Biology", "Evolutionary Biology"], "users"=>["Christina L. Richards", "Ulises Rosas", "Joshua Banta", "Naeha Bhambhra", "Michael D. Purugganan"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1002662.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_the_major_vegetative_stage_principal_components_of_A_thaliana_genome_wide_gene_expression_in_the_field_/321327", "title"=>"Characteristics of the major vegetative stage principal components of <i>A. thaliana</i> genome-wide gene expression in the field.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-04-19 00:22:07"}

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Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[322, 550, 671, 773, 864, 955, 1048, 1135, 1223, 1308, 1387, 1465, 1534, 1602, 1673, 1744, 1813, 1885, 1955, 2026, 2093, 2160, 2228, 2290, 2349]}, {"subject_area"=>"/Biology and life sciences/Ecology", "average_usage"=>[350, 552, 657, 754, 839, 932, 1023, 1103, 1197, 1274, 1359, 1436, 1499, 1564, 1640, 1726, 1794, 1865, 1933, 2021, 2101, 2181, 2239, 2324, 2376]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[333, 576, 707, 814, 908, 1004, 1104, 1197, 1280, 1370, 1449, 1531, 1603, 1673, 1742, 1817, 1886, 1954, 2025, 2098, 2171, 2234, 2304, 2365, 2431]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[331, 557, 677, 777, 868, 960, 1050, 1136, 1223, 1307, 1390, 1466, 1536, 1603, 1673, 1741, 1814, 1889, 1954, 2028, 2096, 2164, 2233, 2305, 2362]}, {"subject_area"=>"/Ecology and environmental sciences/Ecology", "average_usage"=>[347, 547, 641, 742, 836, 927, 1016, 1099, 1184, 1267, 1348, 1418, 1484, 1555, 1631, 1705, 1788, 1843, 1917, 1985, 2052, 2115, 2190, 2258, 2333]}]}
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