Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes
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{"title"=>"Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes", "type"=>"journal", "authors"=>[{"first_name"=>"Param Priya", "last_name"=>"Singh", "scopus_author_id"=>"55509715800"}, {"first_name"=>"Jatin", "last_name"=>"Arora", "scopus_author_id"=>"56763632800"}, {"first_name"=>"Hervé", "last_name"=>"Isambert", "scopus_author_id"=>"6602567946"}], "year"=>2015, "source"=>"PLoS Computational Biology", "identifiers"=>{"issn"=>"15537358", "scopus"=>"2-s2.0-84938614149", "pmid"=>"26181593", "doi"=>"10.1371/journal.pcbi.1004394", "pui"=>"605505649", "isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)", "sgr"=>"84938614149"}, "id"=>"736bedd0-e6c1-39aa-acf2-4cd4b1c1e0fd", "abstract"=>"Whole genome duplications (WGD) have now been firmly established in all major eukaryotic kingdoms. In particular, all vertebrates descend from two rounds of WGDs, that occurred in their jawless ancestor some 500 MY ago. Paralogs retained from WGD, also coined 'ohnologs' after Susumu Ohno, have been shown to be typically associated with development, signaling and gene regulation. Ohnologs, which amount to about 20 to 35% of genes in the human genome, have also been shown to be prone to dominant deleterious mutations and frequently implicated in cancer and genetic diseases. Hence, identifying ohnologs is central to better understand the evolution of vertebrates and their susceptibility to genetic diseases. Early computational analyses to identify vertebrate ohnologs relied on content-based synteny comparisons between the human genome and a single invertebrate outgroup genome or within the human genome itself. These approaches are thus limited by lineage specific rearrangements in individual genomes. We report, in this study, the identification of vertebrate ohnologs based on the quantitative assessment and integration of synteny conservation between six amniote vertebrates and six invertebrate outgroups. Such a synteny comparison across multiple genomes is shown to enhance the statistical power of ohnolog identification in vertebrates compared to earlier approaches, by overcoming lineage specific genome rearrangements. Ohnolog gene families can be browsed and downloaded for three statistical confidence levels or recompiled for specific, user-defined, significance criteria at http://ohnologs.curie.fr/. In the light of the importance of WGD on the genetic makeup of vertebrates, our analysis provides a useful resource for researchers interested in gaining further insights on vertebrate evolution and genetic diseases.", "link"=>"http://www.mendeley.com/research/identification-ohnolog-genes-originating-whole-genome-duplication-early-vertebrates-based-synteny-co", "reader_count"=>81, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>6, "Researcher"=>25, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>2, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>13, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>6, "Researcher"=>25, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>2, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>13, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>18, "Mathematics"=>1, "Agricultural and Biological Sciences"=>47, "Medicine and Dentistry"=>3, "Neuroscience"=>3, "Physics and Astronomy"=>1, "Psychology"=>1, "Social Sciences"=>1, "Computer Science"=>4, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Neuroscience"=>{"Neuroscience"=>3}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>47}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>18}, "Mathematics"=>{"Mathematics"=>1}}, "reader_count_by_country"=>{"Canada"=>2, "Sweden"=>1, "United States"=>2, "Taiwan"=>1, "Finland"=>1, "Brazil"=>1, "Italy"=>1, "United Kingdom"=>2, "France"=>1, "Germany"=>1, "India"=>1, "Spain"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2179440"], "description"=>"<p>(A) Gene Ontology enrichment for four amniote ohnolog datasets from the relaxed criteria. From top to bottom, the top 25 enriched GO terms, sorted on the basis of average rank across the four genomes. Bubble sizes are proportional to the rank (p-value) of the term for each genome. (B) Ohnolog association to cancer and genetic diseases in human. Ohnolog enrichment is especially significant for core cancer genes, autosomal dominant disease genes and genes with autoinhibitory protein folds, see text, in agreement with earlier reports [<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004394#pcbi.1004394.ref005\" target=\"_blank\">5</a>, <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004394#pcbi.1004394.ref006\" target=\"_blank\">6</a>, <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004394#pcbi.1004394.ref015\" target=\"_blank\">15</a>].</p>", "links"=>[], "tags"=>["Whole Genome Duplication", "Ohnolog gene families", "500 MY", "genome duplications", "Ohnolog Genes Originating", "jawless ancestor", "ohnolog identification", "wgd", "amniote vertebrates", "Multiple Genomes", "significance criteria", "Susumu Ohno", "Synteny Comparison", "confidence levels", "synteny conservation", "eukaryotic kingdoms", "Gene regulation", "invertebrate outgroups", "genome rearrangements", "invertebrate outgroup genome"], "article_id"=>1486110, "categories"=>["Biological Sciences"], "users"=>["Param Priya Singh", "Jatin Arora", "Hervé Isambert"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004394.g005", "stats"=>{"downloads"=>4, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ohnolog_association_to_cancer_and_diseases_in_human_/1486110", "title"=>"Ohnolog association to cancer and diseases in human.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-16 03:28:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2179437"], "description"=>"<p>Flowchart of the algorithm to identify ohnolog pairs and construct ohnolog families for a single vertebrate genome using content-based synteny comparison with multiple outgroup genomes (left panel) and self-comparison (right panel), see main text and <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004394#pcbi.1004394.s001\" target=\"_blank\">S1 Text</a> for details.</p>", "links"=>[], "tags"=>["Whole Genome Duplication", "Ohnolog gene families", "500 MY", "genome duplications", "Ohnolog Genes Originating", "jawless ancestor", "ohnolog identification", "wgd", "amniote vertebrates", "Multiple Genomes", "significance criteria", "Susumu Ohno", "Synteny Comparison", "confidence levels", "synteny conservation", "eukaryotic kingdoms", "Gene regulation", "invertebrate outgroups", "genome rearrangements", "invertebrate outgroup genome"], "article_id"=>1486107, "categories"=>["Biological Sciences"], "users"=>["Param Priya Singh", "Jatin Arora", "Hervé Isambert"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004394.g002", "stats"=>{"downloads"=>4, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Flowchart_of_the_algorithm_to_identify_ohnologs_/1486107", "title"=>"Flowchart of the algorithm to identify ohnologs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-16 03:28:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2179436"], "description"=>"<p>Evolution after WGD and identification of ohnologs using content-based synteny comparison. The genomes of three lineages sharing a common ancestor are shown. Orthologs and paralogs have been depicted by the same color. The WGD lineage (A) underwent whole genome duplication (B) followed by non-functionalization (C) and genome rearrangements (D) leading to the current intragenomic content-based synteny (I). By contrast, the two outgroup genomes without WGD (E, G) experienced lineage specific genome rearrangements (F, H) leading to 1-to-2 content-based synteny pattern with the WGD lineage (J, K). Note, that some ohnolog pairs (D) are only identified by one of the two outgroups (J or K) due to lineage specific rearrangements.</p>", "links"=>[], "tags"=>["Whole Genome Duplication", "Ohnolog gene families", "500 MY", "genome duplications", "Ohnolog Genes Originating", "jawless ancestor", "ohnolog identification", "wgd", "amniote vertebrates", "Multiple Genomes", "significance criteria", "Susumu Ohno", "Synteny Comparison", "confidence levels", "synteny conservation", "eukaryotic kingdoms", "Gene regulation", "invertebrate outgroups", "genome rearrangements", "invertebrate outgroup genome"], "article_id"=>1486106, "categories"=>["Biological Sciences"], "users"=>["Param Priya Singh", "Jatin Arora", "Hervé Isambert"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004394.g001", "stats"=>{"downloads"=>1, "page_views"=>41, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evolution_after_WGD_and_identification_of_ohnologs_/1486106", "title"=>"Evolution after WGD and identification of ohnologs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-16 03:28:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2179439"], "description"=>"<p>A six-way Venn diagram showing the distribution in percentages of the ohnologs identified in at least one amniote and predicted from the relaxed criteria. 36.6% of ohnologs are found in all six amniotes. Each shaded sectors in red contributes to more than 2% of all consensus ohnologs in amniotes (numbers of ohnologs are given in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004394#pcbi.1004394.s011\" target=\"_blank\">S10 Fig</a>).</p>", "links"=>[], "tags"=>["Whole Genome Duplication", "Ohnolog gene families", "500 MY", "genome duplications", "Ohnolog Genes Originating", "jawless ancestor", "ohnolog identification", "wgd", "amniote vertebrates", "Multiple Genomes", "significance criteria", "Susumu Ohno", "Synteny Comparison", "confidence levels", "synteny conservation", "eukaryotic kingdoms", "Gene regulation", "invertebrate outgroups", "genome rearrangements", "invertebrate outgroup genome"], "article_id"=>1486109, "categories"=>["Biological Sciences"], "users"=>["Param Priya Singh", "Jatin Arora", "Hervé Isambert"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004394.g004", "stats"=>{"downloads"=>5, "page_views"=>39, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Venn_diagram_of_the_distribution_of_amniote_ohnologs_/1486109", "title"=>"Venn diagram of the distribution of amniote ohnologs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-16 03:28:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2179438"], "description"=>"<p>A six-way Venn diagram showing the distribution in percentages of the 7,715 of the total 8,178 human ohnolog pairs that are identified by at least one outgroup and predicted from the relaxed criteria. Only 3.8% of human ohnolog pairs are identified by all outgroup. Each of the shaded sectors in green contributes to more than 2% of all ohnolog pairs (numbers of ohnolog pairs are given in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004394#pcbi.1004394.s009\" target=\"_blank\">S8 Fig</a>).</p>", "links"=>[], "tags"=>["Whole Genome Duplication", "Ohnolog gene families", "500 MY", "genome duplications", "Ohnolog Genes Originating", "jawless ancestor", "ohnolog identification", "wgd", "amniote vertebrates", "Multiple Genomes", "significance criteria", "Susumu Ohno", "Synteny Comparison", "confidence levels", "synteny conservation", "eukaryotic kingdoms", "Gene regulation", "invertebrate outgroups", "genome rearrangements", "invertebrate outgroup genome"], "article_id"=>1486108, "categories"=>["Biological Sciences"], "users"=>["Param Priya Singh", "Jatin Arora", "Hervé Isambert"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1004394.g003", "stats"=>{"downloads"=>4, "page_views"=>35, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Venn_diagram_of_distribution_of_human_ohnologs_with_respect_to_outgroups_/1486108", "title"=>"Venn diagram of distribution of human ohnologs with respect to outgroups.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-07-16 03:28:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2179441", "https://ndownloader.figshare.com/files/2179442", "https://ndownloader.figshare.com/files/2179443", "https://ndownloader.figshare.com/files/2179444", "https://ndownloader.figshare.com/files/2179445", "https://ndownloader.figshare.com/files/2179446", "https://ndownloader.figshare.com/files/2179447", "https://ndownloader.figshare.com/files/2179448", "https://ndownloader.figshare.com/files/2179449", "https://ndownloader.figshare.com/files/2179450", "https://ndownloader.figshare.com/files/2179451", "https://ndownloader.figshare.com/files/2179452", "https://ndownloader.figshare.com/files/2179453", "https://ndownloader.figshare.com/files/2179454"], "description"=>"<div><p>Whole genome duplications (WGD) have now been firmly established in all major eukaryotic kingdoms. In particular, all vertebrates descend from two rounds of WGDs, that occurred in their jawless ancestor some 500 MY ago. Paralogs retained from WGD, also coined ‘ohnologs’ after Susumu Ohno, have been shown to be typically associated with development, signaling and gene regulation. Ohnologs, which amount to about 20 to 35% of genes in the human genome, have also been shown to be prone to dominant deleterious mutations and frequently implicated in cancer and genetic diseases. Hence, identifying ohnologs is central to better understand the evolution of vertebrates and their susceptibility to genetic diseases. Early computational analyses to identify vertebrate ohnologs relied on content-based synteny comparisons between the human genome and a single invertebrate outgroup genome or within the human genome itself. These approaches are thus limited by lineage specific rearrangements in individual genomes. We report, in this study, the identification of vertebrate ohnologs based on the quantitative assessment and integration of synteny conservation between six amniote vertebrates and six invertebrate outgroups. Such a synteny comparison across multiple genomes is shown to enhance the statistical power of ohnolog identification in vertebrates compared to earlier approaches, by overcoming lineage specific genome rearrangements. Ohnolog gene families can be browsed and downloaded for three statistical confidence levels or recompiled for specific, user-defined, significance criteria at <a href=\"http://ohnologs.curie.fr/\" target=\"_blank\">http://ohnologs.curie.fr/</a>. In the light of the importance of WGD on the genetic makeup of vertebrates, our analysis provides a useful resource for researchers interested in gaining further insights on vertebrate evolution and genetic diseases.</p></div>", "links"=>[], "tags"=>["Whole Genome Duplication", "Ohnolog gene families", "500 MY", "genome duplications", "Ohnolog Genes Originating", "jawless ancestor", "ohnolog identification", "wgd", "amniote vertebrates", "Multiple Genomes", "significance criteria", "Susumu Ohno", "Synteny Comparison", "confidence levels", "synteny conservation", "eukaryotic kingdoms", "Gene regulation", "invertebrate outgroups", "genome rearrangements", "invertebrate outgroup genome"], "article_id"=>1486111, "categories"=>["Biological Sciences"], "users"=>["Param Priya Singh", "Jatin Arora", "Hervé Isambert"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1004394.s001", "https://dx.doi.org/10.1371/journal.pcbi.1004394.s002", "https://dx.doi.org/10.1371/journal.pcbi.1004394.s003", "https://dx.doi.org/10.1371/journal.pcbi.1004394.s004", "https://dx.doi.org/10.1371/journal.pcbi.1004394.s005", "https://dx.doi.org/10.1371/journal.pcbi.1004394.s006", "https://dx.doi.org/10.1371/journal.pcbi.1004394.s007", "https://dx.doi.org/10.1371/journal.pcbi.1004394.s008", "https://dx.doi.org/10.1371/journal.pcbi.1004394.s009", "https://dx.doi.org/10.1371/journal.pcbi.1004394.s010", "https://dx.doi.org/10.1371/journal.pcbi.1004394.s011", "https://dx.doi.org/10.1371/journal.pcbi.1004394.s012", "https://dx.doi.org/10.1371/journal.pcbi.1004394.s013", "https://dx.doi.org/10.1371/journal.pcbi.1004394.s014"], "stats"=>{"downloads"=>27, "page_views"=>58, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_Ohnolog_Genes_Originating_from_Whole_Genome_Duplication_in_Early_Vertebrates_Based_on_Synteny_Comparison_across_Multiple_Genomes_/1486111", "title"=>"Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-07-16 03:28:35"}

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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