Width of Gene Expression Profile Drives Alternative Splicing
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{"title"=>"Width of gene expression profile drives alternative splicing", "type"=>"journal", "authors"=>[{"first_name"=>"Daniel", "last_name"=>"Wegmann", "scopus_author_id"=>"15752040200"}, {"first_name"=>"Isabelle", "last_name"=>"Dupanloup", "scopus_author_id"=>"6602711154"}, {"first_name"=>"Laurent", "last_name"=>"Excoffier", "scopus_author_id"=>"7004470075"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-56349149681", "sgr"=>"56349149681", "doi"=>"10.1371/journal.pone.0003587", "pui"=>"352694724", "pmid"=>"18974852", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"cafbbd56-726e-36ef-9119-c420a0cc8371", "abstract"=>"Alternative splicing generates an enormous amount of functional and proteomic diversity in metazoan organisms. This process is probably central to the macromolecular and cellular complexity of higher eukaryotes. While most studies have focused on the molecular mechanism triggering and controlling alternative splicing, as well as on its incidence in different species, its maintenance and evolution within populations has been little investigated. Here, we propose to address these questions by comparing the structural characteristics as well as the functional and transcriptional profiles of genes with monomorphic or polymorphic splicing, referred to as MS and PS genes, respectively. We find that MS and PS genes differ particularly in the number of tissues and cell types where they are expressed.We find a striking deficit of PS genes on the sex chromosomes, particularly on the Y chromosome where it is shown not to be due to the observed lower breadth of expression of genes on that chromosome. The development of a simple model of evolution of cis-regulated alternative splicing leads to predictions in agreement with these observations. It further predicts the conditions for the emergence and the maintenance of cis-regulated alternative splicing, which are both favored by the tissue specific expression of splicing variants. We finally propose that the width of the gene expression profile is an essential factor for the acquisition of new transcript isoforms that could later be maintained by a new form of balancing selection.", "link"=>"http://www.mendeley.com/research/width-gene-expression-profile-drives-alternative-splicing", "reader_count"=>41, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>15, "Student > Master"=>4, "Student > Bachelor"=>2, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>15, "Student > Master"=>4, "Student > Bachelor"=>2, "Lecturer"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>4, "Mathematics"=>1, "Agricultural and Biological Sciences"=>29, "Medicine and Dentistry"=>2, "Computer Science"=>1, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>29}, "Computer Science"=>{"Computer Science"=>1}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Netherlands"=>1, "Slovenia"=>1, "Australia"=>1, "Switzerland"=>3, "Germany"=>1, "India"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/916828"], "description"=>"<p>A. Functional classification of genes according to the GO ontology. Note that a gene may be associated with more than one function and hence may belong to more than one functional group. The chart shows a clear and positive relationship between the number of distinct biological processes and the number of cellular components in which gene products are involved. Top (right): histogram of the number of distinct biological processes (cellular components) for MS and PS genes. The list of cellular components and biological processes is shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003587#pone.0003587.s004\" target=\"_blank\">Figure S4</a>. B. Expression profiles of MS and PS genes in humans using ESTs and the eVOC ontology. The chart shows a clear and positive relationship between the number of distinct anatomical systems and the number of cell types in which the genes are expressed. Top (right): histogram of the number of distinct anatomical systems (cell types) for MS and PS genes. The cell types and the list of anatomical systems are given in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0003587#pone.0003587.s010\" target=\"_blank\">Table S2</a>. The circle areas are proportional to the number of genes. Information for MS and PS genes is shown in white and black, respectively.</p>", "links"=>[], "tags"=>["classification", "profiles", "ms", "bars", "ps", "genes"], "article_id"=>587277, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Daniel Wegmann", "Isabelle Dupanloup", "Laurent Excoffier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003587.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functional_classification_and_expression_profiles_of_MS_white_bars_and_circles_and_PS_black_bars_and_circles_genes_in_humans_/587277", "title"=>"Functional classification and expression profiles of MS (white bars and circles) and PS (black bars and circles) genes in humans.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-31 02:01:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/453137", "https://ndownloader.figshare.com/files/453288", "https://ndownloader.figshare.com/files/453434", "https://ndownloader.figshare.com/files/453523", "https://ndownloader.figshare.com/files/453632", "https://ndownloader.figshare.com/files/453791", "https://ndownloader.figshare.com/files/453953", "https://ndownloader.figshare.com/files/454087", "https://ndownloader.figshare.com/files/454305", "https://ndownloader.figshare.com/files/454332", "https://ndownloader.figshare.com/files/454351", "https://ndownloader.figshare.com/files/454368"], "description"=>"<div><p>Alternative splicing generates an enormous amount of functional and proteomic diversity in metazoan organisms. This process is probably central to the macromolecular and cellular complexity of higher eukaryotes. While most studies have focused on the molecular mechanism triggering and controlling alternative splicing, as well as on its incidence in different species, its maintenance and evolution within populations has been little investigated. Here, we propose to address these questions by comparing the structural characteristics as well as the functional and transcriptional profiles of genes with monomorphic or polymorphic splicing, referred to as MS and PS genes, respectively. We find that MS and PS genes differ particularly in the number of tissues and cell types where they are expressed.We find a striking deficit of PS genes on the sex chromosomes, particularly on the Y chromosome where it is shown not to be due to the observed lower breadth of expression of genes on that chromosome. The development of a simple model of evolution of cis-regulated alternative splicing leads to predictions in agreement with these observations. It further predicts the conditions for the emergence and the maintenance of cis-regulated alternative splicing, which are both favored by the tissue specific expression of splicing variants. We finally propose that the width of the gene expression profile is an essential factor for the acquisition of new transcript isoforms that could later be maintained by a new form of balancing selection.</p></div>", "links"=>[], "tags"=>["width", "drives", "splicing"], "article_id"=>149278, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Daniel Wegmann", "Isabelle Dupanloup", "Laurent Excoffier"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0003587.s001", "https://dx.doi.org/10.1371/journal.pone.0003587.s002", "https://dx.doi.org/10.1371/journal.pone.0003587.s003", "https://dx.doi.org/10.1371/journal.pone.0003587.s004", "https://dx.doi.org/10.1371/journal.pone.0003587.s005", "https://dx.doi.org/10.1371/journal.pone.0003587.s006", "https://dx.doi.org/10.1371/journal.pone.0003587.s007", "https://dx.doi.org/10.1371/journal.pone.0003587.s008", "https://dx.doi.org/10.1371/journal.pone.0003587.s009", "https://dx.doi.org/10.1371/journal.pone.0003587.s010", "https://dx.doi.org/10.1371/journal.pone.0003587.s011", "https://dx.doi.org/10.1371/journal.pone.0003587.s012"], "stats"=>{"downloads"=>16, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Width_of_Gene_Expression_Profile_Drives_Alternative_Splicing/149278", "title"=>"Width of Gene Expression Profile Drives Alternative Splicing", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-10-31 02:34:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/917117"], "description"=>"<p>Structure length and number of exons for human genes.</p>", "links"=>[], "tags"=>["exons"], "article_id"=>587579, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Daniel Wegmann", "Isabelle Dupanloup", "Laurent Excoffier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003587.t001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Structure_length_and_number_of_exons_for_human_genes_/587579", "title"=>"Structure length and number of exons for human genes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-10-31 02:06:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/917101"], "description"=>"<p>Orthologs in humans and mice tend to belong to the same splicing class (Fisher exact test of homogeneity, p<0.001).</p>", "links"=>[], "tags"=>["splicing", "genes"], "article_id"=>587555, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Daniel Wegmann", "Isabelle Dupanloup", "Laurent Excoffier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003587.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conservation_of_splicing_ability_for_genes_between_human_and_mouse_/587555", "title"=>"Conservation of splicing ability for genes between human and mouse.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-10-31 02:05:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/917163"], "description"=>"<p>Expression evidence for human genes.</p>", "links"=>[], "tags"=>["genetics and genomics", "evolutionary biology/genomics", "genetics and genomics/functional genomics", "genetics and genomics/gene expression", "genetics and genomics/genomics", "evolutionary biology/human evolution"], "article_id"=>587618, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Daniel Wegmann", "Isabelle Dupanloup", "Laurent Excoffier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003587.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_evidence_for_human_genes_/587618", "title"=>"Expression evidence for human genes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-10-31 02:06:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/917042"], "description"=>"<p>Colored zones correspond to parameter areas where alternative splicing can be maintained by balancing selection. Equilibrium frequency (<i>p</i>) can vary between 0 (blue) and 1 (red).</p>", "links"=>[], "tags"=>["specificity"], "article_id"=>587498, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Daniel Wegmann", "Isabelle Dupanloup", "Laurent Excoffier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003587.g005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effect_of_tissue_specificity_on_the_maintenance_of_alternative_slicing_/587498", "title"=>"Effect of tissue specificity on the maintenance of alternative slicing.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-31 02:04:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/917193"], "description"=>"1<p>Mean number of splicing events per gene.</p>2<p>Proportion of genes showing the corresponding type of splicing variants.</p>", "links"=>[], "tags"=>["splicing", "events", "ps", "genes", "humans"], "article_id"=>587653, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Daniel Wegmann", "Isabelle Dupanloup", "Laurent Excoffier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003587.t002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_splicing_events_for_PS_genes_in_humans_and_mice_/587653", "title"=>"Number of splicing events for PS genes in humans and mice.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-10-31 02:07:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/916747"], "description"=>"<p>A. Contrast between the distributions of MS (white bars) and PS genes (black bars) across chromosomes, which are significantly different (χ<sup>2</sup> = 118.387, df = 23, p<0.001). B. Chromosomal distribution of genes that cannot be assigned ot the MS or PS categories. The ratio of uncharacterized genes on the total number of ENSEMBL genes (grey dashed line) is approximately constant across chromosomes. The ratio of PS genes on MS genes (black dotted line) clearly drops for the Y chromosome and to a lesser extent for the X chromosome.</p>", "links"=>[], "tags"=>["ms", "ps", "genes"], "article_id"=>587205, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Daniel Wegmann", "Isabelle Dupanloup", "Laurent Excoffier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003587.g001", "stats"=>{"downloads"=>4, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Chromosomal_distribution_of_MS_and_PS_genes_in_humans_/587205", "title"=>"Chromosomal distribution of MS and PS genes in humans.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-31 02:00:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/916952"], "description"=>"<p>See text for the definition of the other parameters.</p>", "links"=>[], "tags"=>["splicing", "variant", "specificity"], "article_id"=>587411, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Daniel Wegmann", "Isabelle Dupanloup", "Laurent Excoffier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003587.g004", "stats"=>{"downloads"=>4, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Population_fitness_landscape_z_axis_as_a_function_of_the_frequency_p_of_the_alternative_splicing_variant_P_1_and_its_specificity_for_tissue_T_1_945_11_/587411", "title"=>"Population fitness landscape (z-axis) as a function of the frequency (<i>p</i>) of the alternative splicing variant <i>P</i><sub>1</sub>, and its specificity for tissue <i>T</i><sub>1</sub> (<i>α</i><sub>11</sub>).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-31 02:03:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/916887"], "description"=>"<p>The number of anatomical systems is shown in light grey and the number of cell types is indicated in dark grey. The width of the boxes is proportional to the square-root of the number of genes in each group. The correlation between the number of splicing events and the width of the expression profile for PS genes is highly significant (anatomical systems: <i>r</i> = 0.224, <i>p</i><0.001; cell types: <i>r</i> = 0.238, <i>p</i><0.001).</p>", "links"=>[], "tags"=>["splicing", "events", "ps", "genes"], "article_id"=>587346, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Daniel Wegmann", "Isabelle Dupanloup", "Laurent Excoffier"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0003587.g003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Box_plot_of_the_pattern_of_gene_expression_as_a_function_of_the_number_of_splicing_events_for_PS_genes_in_humans_/587346", "title"=>"Box plot of the pattern of gene expression as a function of the number of splicing events for PS genes in humans.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-10-31 02:02:26"}

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Relative Metric

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