Faster-X Evolution of Gene Expression in Drosophila
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{"title"=>"Faster-X Evolution of Gene Expression in Drosophila", "type"=>"journal", "authors"=>[{"first_name"=>"Richard P.", "last_name"=>"Meisel", "scopus_author_id"=>"22035562200"}, {"first_name"=>"John H.", "last_name"=>"Malone", "scopus_author_id"=>"7202068178"}, {"first_name"=>"Andrew G.", "last_name"=>"Clark", "scopus_author_id"=>"7404479646"}], "year"=>2012, "source"=>"PLoS Genetics", "identifiers"=>{"issn"=>"15537390", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)", "pmid"=>"23071459", "scopus"=>"2-s2.0-84868101450", "pui"=>"365953648", "doi"=>"10.1371/journal.pgen.1003013", "sgr"=>"84868101450"}, "id"=>"7bf1aff7-cc0c-3684-ad89-f5edb256ef43", "abstract"=>"DNA sequences on X chromosomes often have a faster rate of evolution when compared to similar loci on the autosomes, and well articulated models provide reasons why the X-linked mode of inheritance may be responsible for the faster evolution of X-linked genes. We analyzed microarray and RNA-seq data collected from females and males of six Drosophila species and found that the expression levels of X-linked genes also diverge faster than autosomal gene expression, similar to the \"faster-X\" effect often observed in DNA sequence evolution. Faster-X evolution of gene expression was recently described in mammals, but it was limited to the evolutionary lineages shortly following the creation of the therian X chromosome. In contrast, we detect a faster-X effect along both deep lineages and those on the tips of the Drosophila phylogeny. In Drosophila males, the dosage compensation complex (DCC) binds the X chromosome, creating a unique chromatin environment that promotes the hyper-expression of X-linked genes. We find that DCC binding, chromatin environment, and breadth of expression are all predictive of the rate of gene expression evolution. In addition, estimates of the intraspecific genetic polymorphism underlying gene expression variation suggest that X-linked expression levels are not under relaxed selective constraints. We therefore hypothesize that the faster-X evolution of gene expression is the result of the adaptive fixation of beneficial mutations at X-linked loci that change expression level in cis. This adaptive faster-X evolution of gene expression is limited to genes that are narrowly expressed in a single tissue, suggesting that relaxed pleiotropic constraints permit a faster response to selection. Finally, we present a conceptional framework to explain faster-X expression evolution, and we use this framework to examine differences in the faster-X effect between Drosophila and mammals.", "link"=>"http://www.mendeley.com/research/fasterx-evolution-gene-expression-drosophila-1", "reader_count"=>66, "reader_count_by_academic_status"=>{"Unspecified"=>4, "Professor > Associate Professor"=>6, "Researcher"=>16, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>3, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>4, "Professor > Associate Professor"=>6, "Researcher"=>16, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>3, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>53, "Medicine and Dentistry"=>1, "Social Sciences"=>1, "Computer Science"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>53}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>5}}, "reader_count_by_country"=>{"Sweden"=>3, "United States"=>4, "Switzerland"=>1, "Spain"=>1}, "group_count"=>5}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/559855"], "description"=>"<p>Boxplots show the pairwise divergence in expression between 1∶1∶1 orthologs in the <i>D. melanogaster</i> (mel) and <i>D. yakuba</i> (yak) or <i>D. ananassae</i> (ana) genomes measured in whole females and males (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003013#pgen-1003013-g005\" target=\"_blank\">Figure 5</a>, <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003013#pgen-1003013-g006\" target=\"_blank\">Figure 6</a>). X-linked (X, red) and Autosomal (A) genes were assigned to transcriptionally active and repressive chromatin based on the results of experiments in S2 cells (for the results from BG3 cells see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003013#pgen.1003013.s015\" target=\"_blank\">Figure S15</a>). Groups of genes whose pairwise divergence is greater or less (v) than the rest of the genome are marked. Subsets of narrowly expressed genes whose pairwise divergence is significantly different than all other narrowly expressed genes are marked (N). The same was done for subsets of genes in repressive chromatin (R). Significant differences between X-linked and autosomal genes in the same chromatin state and with the same expression breadth are marked with asterisks. Mann-Whitney U tests were used to assess significant differences (one symbol = , two symbols = , three symbols = , four symbols = , five symbols = ).</p>", "links"=>[], "tags"=>["faster-x", "narrowly", "genes", "transcriptionally", "repressive"], "article_id"=>230349, "categories"=>["Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Richard P. Meisel", "John H. Malone", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003013.g008", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_faster_X_effect_is_limited_to_narrowly_expressed_genes_in_transcriptionally_repressive_chromatin_/230349", "title"=>"The faster-X effect is limited to narrowly expressed genes in transcriptionally repressive chromatin.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-11 00:05:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/297733", "https://ndownloader.figshare.com/files/297802", "https://ndownloader.figshare.com/files/297839", "https://ndownloader.figshare.com/files/297884", "https://ndownloader.figshare.com/files/297926", "https://ndownloader.figshare.com/files/298055", "https://ndownloader.figshare.com/files/298251", "https://ndownloader.figshare.com/files/298490", "https://ndownloader.figshare.com/files/298546", "https://ndownloader.figshare.com/files/298761", "https://ndownloader.figshare.com/files/298831", "https://ndownloader.figshare.com/files/298898", "https://ndownloader.figshare.com/files/299104", "https://ndownloader.figshare.com/files/299330", "https://ndownloader.figshare.com/files/299487", "https://ndownloader.figshare.com/files/299558", "https://ndownloader.figshare.com/files/299703", "https://ndownloader.figshare.com/files/299891", "https://ndownloader.figshare.com/files/300045"], "description"=>"<div><p>DNA sequences on X chromosomes often have a faster rate of evolution when compared to similar loci on the autosomes, and well articulated models provide reasons why the X-linked mode of inheritance may be responsible for the faster evolution of X-linked genes. We analyzed microarray and RNA–seq data collected from females and males of six <em>Drosophila</em> species and found that the expression levels of X-linked genes also diverge faster than autosomal gene expression, similar to the “faster-X” effect often observed in DNA sequence evolution. Faster-X evolution of gene expression was recently described in mammals, but it was limited to the evolutionary lineages shortly following the creation of the therian X chromosome. In contrast, we detect a faster-X effect along both deep lineages and those on the tips of the <em>Drosophila</em> phylogeny. In <em>Drosophila</em> males, the dosage compensation complex (DCC) binds the X chromosome, creating a unique chromatin environment that promotes the hyper-expression of X-linked genes. We find that DCC binding, chromatin environment, and breadth of expression are all predictive of the rate of gene expression evolution. In addition, estimates of the intraspecific genetic polymorphism underlying gene expression variation suggest that X-linked expression levels are not under relaxed selective constraints. We therefore hypothesize that the faster-X evolution of gene expression is the result of the adaptive fixation of beneficial mutations at X-linked loci that change expression level in <em>cis</em>. This adaptive faster-X evolution of gene expression is limited to genes that are narrowly expressed in a single tissue, suggesting that relaxed pleiotropic constraints permit a faster response to selection. Finally, we present a conceptional framework to explain faster-X expression evolution, and we use this framework to examine differences in the faster-X effect between <em>Drosophila</em> and mammals.</p> </div>", "links"=>[], "tags"=>["faster-x"], "article_id"=>118697, "categories"=>["Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Richard P. Meisel", "John H. Malone", "Andrew G. Clark"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1003013.s001", "https://dx.doi.org/10.1371/journal.pgen.1003013.s002", "https://dx.doi.org/10.1371/journal.pgen.1003013.s003", "https://dx.doi.org/10.1371/journal.pgen.1003013.s004", "https://dx.doi.org/10.1371/journal.pgen.1003013.s005", "https://dx.doi.org/10.1371/journal.pgen.1003013.s006", "https://dx.doi.org/10.1371/journal.pgen.1003013.s007", "https://dx.doi.org/10.1371/journal.pgen.1003013.s008", "https://dx.doi.org/10.1371/journal.pgen.1003013.s009", "https://dx.doi.org/10.1371/journal.pgen.1003013.s010", "https://dx.doi.org/10.1371/journal.pgen.1003013.s011", "https://dx.doi.org/10.1371/journal.pgen.1003013.s012", "https://dx.doi.org/10.1371/journal.pgen.1003013.s013", "https://dx.doi.org/10.1371/journal.pgen.1003013.s014", "https://dx.doi.org/10.1371/journal.pgen.1003013.s015", "https://dx.doi.org/10.1371/journal.pgen.1003013.s016", "https://dx.doi.org/10.1371/journal.pgen.1003013.s017", "https://dx.doi.org/10.1371/journal.pgen.1003013.s018", "https://dx.doi.org/10.1371/journal.pgen.1003013.s019"], "stats"=>{"downloads"=>65, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Faster_X_Evolution_of_Gene_Expression_in_Drosophila_/118697", "title"=>"Faster-X Evolution of Gene Expression in <em>Drosophila</em>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-10-11 02:24:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/559225"], "description"=>"<p>Pairwise correlations of gene expression are shown for genes on each chromosome arm, using expression measurements from (A) females or (B) males. In each graph, the solid horizontal line is the genome-wide correlation, and the dashed lines are the 95% confidence interval (CI). Each point represents the correlation for a chromosome arm, and the error bars are the 95% CI. Chromosome arms are represented with their Muller element nomenclature. Muller element A is is the X chromosome (red), and Muller element D is the <i>D. pseudoobscura</i> neo-X chromosome. Species names were abbreviated as follows: mel =  <i>D. melanogaster</i>, yak =  <i>D. yakuba</i>, ana = <i>D. ananassae</i>, pse = <i>D. pseudoobscura</i>, moj = <i>D. mojavensis</i>, vir = <i>D. virilis</i>.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "cell biology", "Evolutionary biology"], "article_id"=>229722, "categories"=>["Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Richard P. Meisel", "John H. Malone", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003013.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Faster_X_evolution_of_gene_expression_/229722", "title"=>"Faster-X evolution of gene expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-11 02:42:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/559303"], "description"=>"<p>Gene expression measurements from head using microarrays were used to calculate the correlation of expression levels between <i>D. melanogaster</i> (mel), <i>D. pseudoobscura</i> (pse), and <i>D. mojavensis</i> (moj). Expression was measured in females (top) and males (bottom). Graphs are the same as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003013#pgen-1003013-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "cell biology", "Evolutionary biology"], "article_id"=>229799, "categories"=>["Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Richard P. Meisel", "John H. Malone", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003013.g002", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Faster_X_evolution_of_gene_expression_measured_in_head_/229799", "title"=>"Faster-X evolution of gene expression measured in head.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-11 02:43:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/559719"], "description"=>"<p>Boxplots show the pairwise divergence in expression between 1∶1∶1 orthologs in the <i>D. melanogaster</i> and <i>D. yakuba</i> or <i>D. ananassae</i> genomes measured in whole females and males (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003013#pgen-1003013-g005\" target=\"_blank\">Figure 5</a>). X-linked (X, red) and autosomal (A) genes were assigned to transcriptionally active and repressive chromatin based on the results of ChIP-chip experiments in one of two cell lines (BG3 and S2) <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003013#pgen.1003013-Kharchenko1\" target=\"_blank\">[65]</a>. Counts of genes in each chromatin state are given for data collected from each of the cell lines in the top left quadrants. Groups of genes whose pairwise divergence is greater () or less (v) than the rest of the genome are marked. Comparisons were also made between genes in active and repressive chromatin on the X chromosome or autosomes, and comparisons were made between autosomal and X-linked genes in active or repressive chromatin. Mann-Whitney U tests were used to assess significant differences (one symbol = , two symbols = , three symbols = , four symbols = ).</p>", "links"=>[], "tags"=>["genes", "transcriptionally", "repressive"], "article_id"=>230214, "categories"=>["Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Richard P. Meisel", "John H. Malone", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003013.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Faster_expression_evolution_of_genes_associated_with_transcriptionally_repressive_chromatin_/230214", "title"=>"Faster expression evolution of genes associated with transcriptionally repressive chromatin.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-11 00:03:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/559423"], "description"=>"<p>Overlaid on each branch of the phylogeny are the branch lengths estimated from the pairwise correlations in expression (measured in whole flies with microarrays) using the Fitch and Margoliash <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003013#pgen.1003013-Fitch1\" target=\"_blank\">[115]</a> method. In each graph, the solid horizontal line is the genome-wide branch length, and the dashed lines are the 95% CI. Each point represents the branch length estimate for a chromosome arm (X is in red), and the error bars are the 95% CI. Bootstrap supports for the nodes are listed in the boxes adjacent to the nodes. The first number, in bold, is the bootstrap support using all orthologs, and the subsequent five values are for genes on each chromosome arm (X is in red). The last value, in italics, is the bootstrap support using genes on the four autosomes (Muller elements B–E). Chromosome arms are represented with their Muller element nomenclature, as described in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003013#pgen-1003013-g001\" target=\"_blank\">Figure 1</a>. The Fitch and Margoliash algorithm treats the phylogeny as unrooted, so there is a single branch length and bootstrap value for the lineage connecting the Sophophora (<i>D. melanogaster</i>, <i>D. yakuba</i>, <i>D. ananassae</i>, and <i>D. pseudoobscura</i>) and Drosophila (<i>D. mojavensis</i> and <i>D. virilis</i>) subgenera. Branch lengths and bootstrap support were estimated using expression measurements from (panel A) females and (panel B) males.</p>", "links"=>[], "tags"=>["estimates", "bootstrap"], "article_id"=>229922, "categories"=>["Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Richard P. Meisel", "John H. Malone", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003013.g004", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Branch_length_estimates_and_bootstrap_support_from_expression_level_divergence_/229922", "title"=>"Branch length estimates and bootstrap support from expression level divergence.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-11 02:45:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/560065"], "description"=>"<p>Factors that contribute to the faster-X evolution of gene expression.</p>", "links"=>[], "tags"=>["faster-x"], "article_id"=>230561, "categories"=>["Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Richard P. Meisel", "John H. Malone", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003013.t001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Factors_that_contribute_to_the_faster_X_evolution_of_gene_expression_/230561", "title"=>"Factors that contribute to the faster-X evolution of gene expression.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-10-11 00:09:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/560026"], "description"=>"<p>Expression level of a gene (dashed blue line) and relative fitness (solid green curve) are plotted for genotypes at a locus with two alleles ( and ). The alleles have additive phenotypic effects, with each copy of increasing expression level. (A) The locus is autosomal with phenotypic and fitness measurements collected in females or males, or it is X-linked with measurements collected in females. (B) The locus is X-linked and not dosage compensated with measurements collected in males.</p>", "links"=>[], "tags"=>["phenotypic"], "article_id"=>230525, "categories"=>["Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Richard P. Meisel", "John H. Malone", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003013.g010", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Additive_phenotypic_effects_fitness_landscapes_and_X_linkage_/230525", "title"=>"Additive phenotypic effects, fitness landscapes, and X-linkage.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-11 00:08:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/559563"], "description"=>"<p>(A) Boxplots show the pairwise divergence in expression between 1∶1∶1 orthologs in the <i>D. melanogaster</i> (mel), <i>D. yakuba</i> (yak), and <i>D. ananassae</i> (ana) genomes measured in whole females (top) and males (bottom) on each chromosome arm. X-linked genes are divided into those that are bound and unbound by the DCC. The counts of genes on each chromosome and DCC bound and unbound genes are given along the x-axis. Boxes extend from the first to the third quartile (interquartile range; IQR), the horizontal line in the middle of the box indicates the median value, and the whiskers represent (outliers are not plotted). Error bars within each box show the location of (where is the sample size), which approximates a 95% CI of the median. The genome-wide average is represented by the horizontal gray line. X-linked genes whose median pairwise divergence is greater () or less (v) than autosomal genes are marked (there is not a significant difference in expression divergence between autosomes). Asterisks indicate significant differences in the medians between X-linked genes bound and unbound by the DCC. Mann-Whitney U tests were used to assess significant differences (one symbol = , two symbols = , three symbols = , four symbols = ). (B) Plots show the correlation between distance from the nearest HAS and the pairwise expression divergence between <i>D. melanogaster</i> (mel) and <i>D. yakuba</i> (yak) or <i>D. ananassae</i> (ana), along with the 95% CI. Expression levels were measured in females (top) and males (bottom). The dashed horizontal line shows the null expectation (). (C) Plots show the correlation between expression level in <i>D. melanogaster</i> and expression divergence between mel and yak or ana for autosomal (A) and X-linked (X, red) genes, along with the 95% CI. Expression levels were measured in females (top) and males (bottom). The solid horizontal line is the genome-wide correlation, and the dashed lines are the 95% CI of the genome-wide value. (D) Plots show the partial correlations between distance from the nearest HAS (dist), pair-wise divergence in expression between 1∶1∶1 orthologs (div), and expression level in <i>D. melanogaster</i> (level). Error bars represent the 95% CI of the partial correlations, estimated by bootstrapping. The dashed horizontal line shows the null expectation ().</p>", "links"=>[], "tags"=>["x-linked", "genes", "regulated"], "article_id"=>230059, "categories"=>["Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Richard P. Meisel", "John H. Malone", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003013.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Faster_expression_evolution_of_X_linked_genes_not_directly_regulated_by_the_DCC_/230059", "title"=>"Faster expression evolution of X-linked genes not directly regulated by the DCC.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-11 00:00:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/559930"], "description"=>"<p>(A) Pairwise correlations of gene expression between the sexes are shown for genes on each chromosome arm, using expression measurements from six species. Correlations are represented as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003013#pgen-1003013-g001\" target=\"_blank\">Figure 1</a>. (B–E) Boxplots show the distribution of of expression level in <i>D. melanogaster</i> females or males for genes with significant heritability. Horizontal dashed lines show the genome-wide average . Asterisks indicate significant differences between subsets of genes. Groups of genes whose is greater or less (v) than the rest of the genome are marked. Mann-Whitney U tests were used to assess significant differences (one symbol = , two symbols = , three symbols = , four symbols = , five symbols = ). (B) Genes were divided into those that are X-linked (X, red) and those that are autosomal (A). (C) X-linked genes were divided into those that are bound by the DCC and those that are not. (D–E) Genes were further divided into (D) those that are broadly or narrowly expressed and (E) those that are in transcriptionally active or repressive (repr) chromatin measured in either BG3 or S2 cells.</p>", "links"=>[], "tags"=>["dcc", "chromatin"], "article_id"=>230428, "categories"=>["Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Richard P. Meisel", "John H. Malone", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003013.g009", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Intraspecific_expression_variation_X_linkage_DCC_binding_expression_breadth_and_chromatin_state_/230428", "title"=>"Intraspecific expression variation, X-linkage, DCC binding, expression breadth, and chromatin state.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-11 00:07:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/559793"], "description"=>"<p>Genes were classified based on their expression breadth, whether they are bound by the DCC, and whether they are in transcriptionally active or repressive (repr) chromatin (based on data from S2 cells). (A) Boxplots show the pairwise divergence in expression between 1∶1∶1 orthologs in the <i>D. melanogaster</i> (mel) and <i>D. yakuba</i> (yak) or <i>D. ananassae</i> (ana) genomes for broadly and narrowly expressed genes (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003013#pgen-1003013-g005\" target=\"_blank\">Figure 5</a>). Mann-Whitney U tests were used to assess significant differences in expression divergence between broadly and narrowly expressed genes (***** ). (B) X-linked broadly expressed (gray) and narrowly expressed (white) genes were divided into those that are bound and unbound by the DCC. (C) Broadly expressed (gray) and narrowly expressed (white) genes were divided into those that are in transcriptionally active and repressive chromatin. (B–C) Fisher's exact test was used to determine if there is a non-random distribution of genes in the four classes.</p>", "links"=>[], "tags"=>["dcc", "chromatin"], "article_id"=>230291, "categories"=>["Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Richard P. Meisel", "John H. Malone", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003013.g007", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Association_between_expression_breadth_DCC_binding_chromatin_state_and_expression_divergence_/230291", "title"=>"Association between expression breadth, DCC binding, chromatin state, and expression divergence.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-11 00:04:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/559360"], "description"=>"<p>Correlations of expression between <i>D. melanogaster</i> (mel) and either <i>D. yakuba</i> (yak) or <i>D. ananassae</i> (ana) are plotted for each chromosome arm using expression measurements from whole females (top) or males (bottom). Genes were included if they are narrowly expressed in non-reproductive tissues (black), female reproductive tissues (purple, top), or male reproductive tissues (purple, bottom). Graphs are the same as in <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003013#pgen-1003013-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["genes", "reproductive"], "article_id"=>229857, "categories"=>["Biological Sciences", "Cell Biology", "Genetics", "Evolutionary Biology"], "users"=>["Richard P. Meisel", "John H. Malone", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1003013.g003", "stats"=>{"downloads"=>0, "page_views"=>110, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Faster_X_expression_evolution_for_genes_expressed_in_male_but_not_female_reproductive_tissues_/229857", "title"=>"Faster-X expression evolution for genes expressed in male, but not female, reproductive tissues.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-10-11 02:44:17"}

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Relative Metric

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