Evolutionary Processes Acting on Candidate cis-Regulatory Regions in Humans Inferred from Patterns of Polymorphism and Divergence
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{"title"=>"Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence", "type"=>"journal", "authors"=>[{"first_name"=>"Dara G.", "last_name"=>"Torgerson", "scopus_author_id"=>"7102422383"}, {"first_name"=>"Adam R.", "last_name"=>"Boyko", "scopus_author_id"=>"22133571100"}, {"first_name"=>"Ryan D.", "last_name"=>"Hernandez", "scopus_author_id"=>"8854158100"}, {"first_name"=>"Amit", "last_name"=>"Indap", "scopus_author_id"=>"16238480700"}, {"first_name"=>"Xiaolan", "last_name"=>"Hu", "scopus_author_id"=>"55441093700"}, {"first_name"=>"Thomas J.", "last_name"=>"White", "scopus_author_id"=>"7402586890"}, {"first_name"=>"John J.", "last_name"=>"Sninsky", "scopus_author_id"=>"7003813994"}, {"first_name"=>"Michele", "last_name"=>"Cargill", "scopus_author_id"=>"6603030077"}, {"first_name"=>"Mark D.", "last_name"=>"Adams", "scopus_author_id"=>"7403905579"}, {"first_name"=>"Carlos D.", "last_name"=>"Bustamante", "scopus_author_id"=>"35228607000"}, {"first_name"=>"Andrew G.", "last_name"=>"Clark", "scopus_author_id"=>"7404479646"}], "year"=>2009, "source"=>"PLoS Genetics", "identifiers"=>{"issn"=>"15537390", "scopus"=>"2-s2.0-70149100044", "sgr"=>"70149100044", "pui"=>"355245426", "isbn"=>"1553-7404", "pmid"=>"19662163", "doi"=>"10.1371/journal.pgen.1000592"}, "id"=>"3bc88f2b-0c34-3e82-ac93-f4852ecad2e0", "abstract"=>"Analysis of polymorphism and divergence in the non-coding portion of the human genome yields crucial information about factors driving the evolution of gene regulation. Candidate cis-regulatory regions spanning more than 15,000 genes in 15 African Americans and 20 European Americans were re-sequenced and aligned to the chimpanzee genome in order to identify potentially functional polymorphism and to characterize and quantify departures from neutral evolution. Distortions of the site frequency spectra suggest a general pattern of selective constraint on conserved non-coding sites in the flanking regions of genes (CNCs). Moreover, there is an excess of fixed differences that cannot be explained by a Gamma model of deleterious fitness effects, suggesting the presence of positive selection on CNCs. Extensions of the McDonald-Kreitman test identified candidate cis-regulatory regions with high probabilities of positive and negative selection near many known human genes, the biological characteristics of which exhibit genome-wide trends that differ from patterns observed in protein-coding regions. Notably, there is a higher probability of positive selection in candidate cis-regulatory regions near genes expressed in the fetal brain, suggesting that a larger portion of adaptive regulatory changes has occurred in genes expressed during brain development. Overall we find that natural selection has played an important role in the evolution of candidate cis-regulatory regions throughout hominid evolution.", "link"=>"http://www.mendeley.com/research/evolutionary-processes-acting-candidate-cisregulatory-regions-humans-inferred-patterns-polymorphism", "reader_count"=>142, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>13, "Researcher"=>43, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>37, "Student > Postgraduate"=>9, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>11, "Lecturer"=>1, "Professor"=>13}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>13, "Researcher"=>43, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>37, "Student > Postgraduate"=>9, "Student > Master"=>7, "Other"=>2, "Student > Bachelor"=>11, "Lecturer"=>1, "Professor"=>13}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Biochemistry, Genetics and Molecular Biology"=>13, "Mathematics"=>1, "Agricultural and Biological Sciences"=>111, "Medicine and Dentistry"=>4, "Neuroscience"=>1, "Philosophy"=>1, "Sports and Recreations"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Social Sciences"=>1, "Computer Science"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Neuroscience"=>{"Neuroscience"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>111}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>4}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Philosophy"=>{"Philosophy"=>1}}, "reader_count_by_country"=>{"Austria"=>1, "Netherlands"=>1, "United States"=>23, "Brazil"=>2, "Italy"=>4, "Mexico"=>1, "Israel"=>1, "Portugal"=>1}, "group_count"=>6}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/888993"], "description"=>"<p>The estimate of γ for intergenic sites is from a comparison to synonymous sites.</p><p>*asymptotes to β→∞.</p>", "links"=>[], "tags"=>["estimates", "models", "mutations", "cncs", "flanking", "regions", "genes", "compared", "intergenic"], "article_id"=>559436, "categories"=>["Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Dara G. Torgerson", "Adam R. Boyko", "Ryan D. Hernandez", "Amit Indap", "Xiaolan Hu", "Thomas J. White", "John J. Sninsky", "Michele Cargill", "Mark D. Adams", "Carlos D. Bustamante", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000592.t003", "stats"=>{"downloads"=>5, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Maximum_likelihood_estimates_of_947_under_various_models_of_fitness_effects_for_mutations_in_CNCs_in_the_flanking_regions_of_genes_as_compared_to_intergenic_sites_/559436", "title"=>"Maximum likelihood estimates of γ under various models of fitness effects for mutations in CNCs in the flanking regions of genes as compared to intergenic sites.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-08-07 02:37:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/888777"], "description"=>"<p>Tissues in bold are those that show a similar trend towards a higher probability of positive selection in both coding and candidate <i>cis</i>-regulatory regions. ** = FDR<5%, * = FDR<10%, NT = no trend with <i>p</i>-value>0.05.</p>", "links"=>[], "tags"=>["novartis", "atlas", "higher", "probability", "regions", "nonsynonymous", "sites", "african", "americans", "european", "mann-whitney"], "article_id"=>559209, "categories"=>["Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Dara G. Torgerson", "Adam R. Boyko", "Ryan D. Hernandez", "Amit Indap", "Xiaolan Hu", "Thomas J. White", "John J. Sninsky", "Michele Cargill", "Mark D. Adams", "Carlos D. Bustamante", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000592.t005", "stats"=>{"downloads"=>8, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tissues_from_the_Novartis_Gene_Atlas_2_data_with_a_higher_mean_probability_of_positive_selection_in_candidate_cis_regulatory_regions_CNCs_and_nonsynonymous_sites_Nonsyn_in_African_Americans_AA_and_European_Americans_EA_p_U_tests_/559209", "title"=>"Tissues from the Novartis Gene Atlas 2 data with a higher mean probability of positive selection in candidate <i>cis</i>-regulatory regions (CNCs) and nonsynonymous sites (Nonsyn) in African Americans (AA) and European Americans (EA) (<i>p</i><0.05, Mann-Whitney <i>U</i>-tests).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-08-07 02:33:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/888648"], "description"=>"<p>Cumulative distributions of (A) the probability of negative selection [Pr(γ)<−0.5] and (B) the probability of positive selection [Pr(γ)>0.5] across different classes of sites, and the distribution of γ in (C) candidate <i>cis</i>-regulatory and nonsynonymous sites, and (D) candidate <i>cis</i>-regulatory and synonymous sites. Data shown is for African Americans from a single, concurrent analysis in mkprf including all classes of sites.</p>", "links"=>[], "tags"=>["signatures", "classes"], "article_id"=>559098, "categories"=>["Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Dara G. Torgerson", "Adam R. Boyko", "Ryan D. Hernandez", "Amit Indap", "Xiaolan Hu", "Thomas J. White", "John J. Sninsky", "Michele Cargill", "Mark D. Adams", "Carlos D. Bustamante", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000592.g005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_comparison_of_signatures_of_selection_between_different_classes_of_sites_/559098", "title"=>"A comparison of signatures of selection between different classes of sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-08-07 02:31:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/888219"], "description"=>"<p>Polymorphism and divergence across pooled sites in African and European Americans.</p>", "links"=>[], "tags"=>["divergence", "pooled", "sites", "african", "european"], "article_id"=>558653, "categories"=>["Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Dara G. Torgerson", "Adam R. Boyko", "Ryan D. Hernandez", "Amit Indap", "Xiaolan Hu", "Thomas J. White", "John J. Sninsky", "Michele Cargill", "Mark D. Adams", "Carlos D. Bustamante", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000592.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Polymorphism_and_divergence_across_pooled_sites_in_African_and_European_Americans_/558653", "title"=>"Polymorphism and divergence across pooled sites in African and European Americans.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-08-07 02:24:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/441126", "https://ndownloader.figshare.com/files/441152", "https://ndownloader.figshare.com/files/441177", "https://ndownloader.figshare.com/files/441194", "https://ndownloader.figshare.com/files/441216", "https://ndownloader.figshare.com/files/441233", "https://ndownloader.figshare.com/files/441258", "https://ndownloader.figshare.com/files/441282", "https://ndownloader.figshare.com/files/441308", "https://ndownloader.figshare.com/files/441339", "https://ndownloader.figshare.com/files/441362", "https://ndownloader.figshare.com/files/441383", "https://ndownloader.figshare.com/files/441415", "https://ndownloader.figshare.com/files/441435", "https://ndownloader.figshare.com/files/441460", "https://ndownloader.figshare.com/files/441485", "https://ndownloader.figshare.com/files/441508", "https://ndownloader.figshare.com/files/441519", "https://ndownloader.figshare.com/files/441533", "https://ndownloader.figshare.com/files/441546", "https://ndownloader.figshare.com/files/441560", "https://ndownloader.figshare.com/files/441578", "https://ndownloader.figshare.com/files/441599", "https://ndownloader.figshare.com/files/441618", "https://ndownloader.figshare.com/files/441641", "https://ndownloader.figshare.com/files/441658", "https://ndownloader.figshare.com/files/441674", "https://ndownloader.figshare.com/files/441679", "https://ndownloader.figshare.com/files/441693", "https://ndownloader.figshare.com/files/441736", "https://ndownloader.figshare.com/files/441771", "https://ndownloader.figshare.com/files/441814"], "description"=>"<div><p>Analysis of polymorphism and divergence in the non-coding portion of the human genome yields crucial information about factors driving the evolution of gene regulation. Candidate <em>cis</em>-regulatory regions spanning more than 15,000 genes in 15 African Americans and 20 European Americans were re-sequenced and aligned to the chimpanzee genome in order to identify potentially functional polymorphism and to characterize and quantify departures from neutral evolution. Distortions of the site frequency spectra suggest a general pattern of selective constraint on conserved non-coding sites in the flanking regions of genes (CNCs). Moreover, there is an excess of fixed differences that cannot be explained by a Gamma model of deleterious fitness effects, suggesting the presence of positive selection on CNCs. Extensions of the McDonald-Kreitman test identified candidate <em>cis</em>-regulatory regions with high probabilities of positive and negative selection near many known human genes, the biological characteristics of which exhibit genome-wide trends that differ from patterns observed in protein-coding regions. Notably, there is a higher probability of positive selection in candidate <em>cis</em>-regulatory regions near genes expressed in the fetal brain, suggesting that a larger portion of adaptive regulatory changes has occurred in genes expressed during brain development. Overall we find that natural selection has played an important role in the evolution of candidate <em>cis</em>-regulatory regions throughout hominid evolution.</p></div>", "links"=>[], "tags"=>["evolutionary", "processes", "acting", "regions", "humans", "inferred", "patterns", "polymorphism", "divergence"], "article_id"=>146948, "categories"=>["Cancer", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Dara G. Torgerson", "Adam R. Boyko", "Ryan D. Hernandez", "Amit Indap", "Xiaolan Hu", "Thomas J. White", "John J. Sninsky", "Michele Cargill", "Mark D. Adams", "Carlos D. Bustamante", "Andrew G. Clark"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000592.s001", "https://dx.doi.org/10.1371/journal.pgen.1000592.s002", "https://dx.doi.org/10.1371/journal.pgen.1000592.s003", "https://dx.doi.org/10.1371/journal.pgen.1000592.s004", "https://dx.doi.org/10.1371/journal.pgen.1000592.s005", "https://dx.doi.org/10.1371/journal.pgen.1000592.s006", "https://dx.doi.org/10.1371/journal.pgen.1000592.s007", "https://dx.doi.org/10.1371/journal.pgen.1000592.s008", "https://dx.doi.org/10.1371/journal.pgen.1000592.s009", "https://dx.doi.org/10.1371/journal.pgen.1000592.s010", "https://dx.doi.org/10.1371/journal.pgen.1000592.s011", "https://dx.doi.org/10.1371/journal.pgen.1000592.s012", "https://dx.doi.org/10.1371/journal.pgen.1000592.s013", "https://dx.doi.org/10.1371/journal.pgen.1000592.s014", "https://dx.doi.org/10.1371/journal.pgen.1000592.s015", "https://dx.doi.org/10.1371/journal.pgen.1000592.s016", "https://dx.doi.org/10.1371/journal.pgen.1000592.s017", "https://dx.doi.org/10.1371/journal.pgen.1000592.s018", "https://dx.doi.org/10.1371/journal.pgen.1000592.s019", "https://dx.doi.org/10.1371/journal.pgen.1000592.s020", "https://dx.doi.org/10.1371/journal.pgen.1000592.s021", "https://dx.doi.org/10.1371/journal.pgen.1000592.s022", "https://dx.doi.org/10.1371/journal.pgen.1000592.s023", "https://dx.doi.org/10.1371/journal.pgen.1000592.s024", "https://dx.doi.org/10.1371/journal.pgen.1000592.s025", "https://dx.doi.org/10.1371/journal.pgen.1000592.s026", "https://dx.doi.org/10.1371/journal.pgen.1000592.s027", "https://dx.doi.org/10.1371/journal.pgen.1000592.s028", "https://dx.doi.org/10.1371/journal.pgen.1000592.s029", "https://dx.doi.org/10.1371/journal.pgen.1000592.s030", "https://dx.doi.org/10.1371/journal.pgen.1000592.s031", "https://dx.doi.org/10.1371/journal.pgen.1000592.s032"], "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Evolutionary_Processes_Acting_on_Candidate_cis_Regulatory_Regions_in_Humans_Inferred_from_Patterns_of_Polymorphism_and_Divergence/146948", "title"=>"Evolutionary Processes Acting on Candidate <em>cis</em>-Regulatory Regions in Humans Inferred from Patterns of Polymorphism and Divergence", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-08-07 01:55:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/888402"], "description"=>"<p>Distribution of the probability that γ falls within 5 categories: strong negative selection (red, γ<−1), weak negative selection (brown, −1<γ<−0.5), nearly neutral (yellow, −0.5<γ<0.5), weak positive selection (purple, 0.5<γ<1), and strong positive selection (blue, γ>1). Data shown is for African Americans from a concurrent analysis including (A) candidate <i>cis</i>-regulatory regions, (B) nonsynonymous sites, and (C) synonymous sites, and an independent analysis including (D) simulated neutral data under the inferred demographic model.</p>", "links"=>[], "tags"=>["estimates"], "article_id"=>558850, "categories"=>["Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Dara G. Torgerson", "Adam R. Boyko", "Ryan D. Hernandez", "Amit Indap", "Xiaolan Hu", "Thomas J. White", "John J. Sninsky", "Michele Cargill", "Mark D. Adams", "Carlos D. Bustamante", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000592.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_specific_estimates_of_selection_in_mkprf_/558850", "title"=>"Gene-specific estimates of selection in mkprf.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-08-07 02:27:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/888300"], "description"=>"<p>Unfolded site frequency spectrum of nonsynonymous, synonymous, and conserved non-coding sites in 15 African Americans (above) and 20 European Americans (below); the data was re-sampled for 16 chromosomes to account for missing data. We used the chimpanzee to infer the ancestral state of each polymorphism, and corrected for ancestral misidentification using the method of Hernandez <i>et al. </i><a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000592#pgen.1000592-Hernandez2\" target=\"_blank\">[64]</a>.</p>", "links"=>[], "tags"=>["spectra", "classes"], "article_id"=>558749, "categories"=>["Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Dara G. Torgerson", "Adam R. Boyko", "Ryan D. Hernandez", "Amit Indap", "Xiaolan Hu", "Thomas J. White", "John J. Sninsky", "Michele Cargill", "Mark D. Adams", "Carlos D. Bustamante", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000592.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Allele_frequency_spectra_for_different_classes_of_sites_/558749", "title"=>"Allele frequency spectra for different classes of sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-08-07 02:25:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/888950"], "description"=>"<p>*significant at the 5% level.</p><p>**significant at the 1% level.</p>", "links"=>[], "tags"=>["segregating", "sites", "15", "african", "americans", "20", "european", "compared", "chimpanzee", "neutrality", "chi-square", "synonymous"], "article_id"=>559385, "categories"=>["Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Dara G. Torgerson", "Adam R. Boyko", "Ryan D. Hernandez", "Amit Indap", "Xiaolan Hu", "Thomas J. White", "John J. Sninsky", "Michele Cargill", "Mark D. Adams", "Carlos D. Bustamante", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000592.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_total_number_of_fixed_and_segregating_sites_in_15_African_Americans_AA_and_20_European_Americans_EA_as_compared_to_the_chimpanzee_PanTro2_along_with_the_ratio_of_fixed_segregating_F_S_sites_the_odds_ratio_or_neutrality_index_and_a_chi_square_test_p_v/559385", "title"=>"The total number of fixed and segregating sites in 15 African Americans (AA) and 20 European Americans (EA) as compared to the chimpanzee (PanTro2), along with the ratio of fixed/segregating (F/S) sites, the odds ratio (or neutrality index), and a chi-square test <i>p</i>-value for the comparison of F/S to synonymous sites.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-08-07 02:36:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/889049"], "description"=>"<p>Low frequency derived alleles were defined as the number of SNPs at a frequency of 1/16 (i.e. frequency <10%) after resampling the data for 16 chromosomes to account for missing data in both African Americans (AA) and European Americans (EA). OR = odds ratio.</p>", "links"=>[], "tags"=>["comparing", "derived", "alleles", "categories", "cncs", "compared", "synonymous", "intergenic"], "article_id"=>559492, "categories"=>["Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Dara G. Torgerson", "Adam R. Boyko", "Ryan D. Hernandez", "Amit Indap", "Xiaolan Hu", "Thomas J. White", "John J. Sninsky", "Michele Cargill", "Mark D. Adams", "Carlos D. Bustamante", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000592.t002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fisher_s_Exact_tests_comparing_the_proportion_of_low_frequency_derived_alleles_between_different_categories_of_CNCs_compared_to_synonymous_and_intergenic_sites_/559492", "title"=>"Fisher's Exact tests comparing the proportion of low frequency derived alleles between different categories of CNCs compared to synonymous and intergenic sites.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-08-07 02:38:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/888498"], "description"=>"<p>There is a significant, yet weak positive correlation between estimates of γ in candidate <i>cis</i>-regulatory regions and nonsynonymous sites in both African Americans (top left) (Kendall's <i>tau</i> = 0.055, <i>p</i> = 1.8×10<sup>−11</sup>), and European Americans (top right) (<i>tau</i> = 0.043, <i>p</i> = 2.9×10<sup>−7</sup>). There is a slightly stronger correlation between synonymous and nonsynonymous sites in both African Americans (bottom left) (<i>tau</i> = 0.096, <i>p</i><10<sup>−16</sup>), and European Americans (bottom right) (<i>tau</i> = 0.087, <i>p</i><10<sup>−16</sup>). Candidate <i>cis</i>-regulatory, synonymous, and nonsynonymous sites were run in a single, concurrent run of mkprf.</p>", "links"=>[], "tags"=>["estimates", "classes", "sites"], "article_id"=>558949, "categories"=>["Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Dara G. Torgerson", "Adam R. Boyko", "Ryan D. Hernandez", "Amit Indap", "Xiaolan Hu", "Thomas J. White", "John J. Sninsky", "Michele Cargill", "Mark D. Adams", "Carlos D. Bustamante", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000592.g004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_in_estimates_of_947_at_different_classes_of_sites_within_a_gene_/558949", "title"=>"Correlation in estimates of γ at different classes of sites within a gene.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-08-07 02:29:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/888835"], "description"=>"<p>CNCs, synonymous, and nonsynonymous sites were analyzed both independently, and in a single concurrent run of mkprf (con), both with no fixed variance on the prior distribution of γ. Nonsynonymous sites were also analyzed by restricting to sites within human and mouse conserved regions (cons). Neutral loci simulated under the inferred AA demographic model were analyzed with a demographic correction, without a demographic correction (null demog), and assuming negative selection on synonymous sites (vs. syn+del). Total genes = genes with at least 1 fixed or polymorphic site, +/− = number of loci simulated under positive and negative selection respectively, CI = 95% credibility interval on the estimate of mean γ.</p>", "links"=>[], "tags"=>["genes", "signatures", "conserved", "non-coding", "sites", "nonsynonymous", "african", "americans", "european", "simulated", "inferred", "aa"], "article_id"=>559268, "categories"=>["Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Dara G. Torgerson", "Adam R. Boyko", "Ryan D. Hernandez", "Amit Indap", "Xiaolan Hu", "Thomas J. White", "John J. Sninsky", "Michele Cargill", "Mark D. Adams", "Carlos D. Bustamante", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000592.t004", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_number_of_genes_showing_strong_signatures_of_positive_and_negative_selection_in_conserved_non_coding_sites_CNCs_synonymous_and_nonsynonymous_sites_Nonsyn_in_African_Americans_AA_and_European_Americans_EA_and_for_simulated_data_Sim_under_the_inferred_/559268", "title"=>"The number of genes showing strong signatures of positive and negative selection in conserved non-coding sites (CNCs), synonymous, and nonsynonymous sites (Nonsyn) in African Americans (AA) and European Americans (EA), and for simulated data (Sim) under the inferred AA demographic model (see Methods).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-08-07 02:34:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/888890"], "description"=>"<p>Gene Ontology terms with higher mean probabilities of positive and negative selection in candidate <i>cis</i>-regulatory regions (CNCs) and nonsynonymous sites (Nonsyn) in African Americans (AA) and European Americans (EA) (FDR<25%, Mann-Whitney <i>U</i> test). ** = FDR<5%, * = FDR<10%.</p>", "links"=>[], "tags"=>["ontology", "higher", "probabilities", "regions", "nonsynonymous", "sites", "african", "americans", "european", "mann-whitney"], "article_id"=>559327, "categories"=>["Infectious Diseases", "Medicine", "Genetics", "Evolutionary Biology"], "users"=>["Dara G. Torgerson", "Adam R. Boyko", "Ryan D. Hernandez", "Amit Indap", "Xiaolan Hu", "Thomas J. White", "John J. Sninsky", "Michele Cargill", "Mark D. Adams", "Carlos D. Bustamante", "Andrew G. Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000592.t006", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_Ontology_terms_with_higher_mean_probabilities_of_positive_and_negative_selection_in_candidate_cis_regulatory_regions_CNCs_and_nonsynonymous_sites_Nonsyn_in_African_Americans_AA_and_European_Americans_EA_FDR_U_test__FDR_/559327", "title"=>"Gene Ontology terms with higher mean probabilities of positive and negative selection in candidate <i>cis</i>-regulatory regions (CNCs) and nonsynonymous sites (Nonsyn) in African Americans (AA) and European Americans (EA) (FDR<25%, Mann-Whitney <i>U</i> test). ** = FDR<5%, * = FDR<10%.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-08-07 02:35:27"}

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Relative Metric

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