Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species
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{"title"=>"Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related drosophila species", "type"=>"journal", "authors"=>[{"first_name"=>"Robert K.", "last_name"=>"Bradley", "scopus_author_id"=>"15051738600"}, {"first_name"=>"Xiao Yong", "last_name"=>"Li", "scopus_author_id"=>"55718273300"}, {"first_name"=>"Cole", "last_name"=>"Trapnell", "scopus_author_id"=>"23486978600"}, {"first_name"=>"Stuart", "last_name"=>"Davidson", "scopus_author_id"=>"57197890368"}, {"first_name"=>"Lior", "last_name"=>"Pachter", "scopus_author_id"=>"7006316240"}, {"first_name"=>"Hou Cheng", "last_name"=>"Chu", "scopus_author_id"=>"24503197800"}, {"first_name"=>"Leath A.", "last_name"=>"Tonkin", "scopus_author_id"=>"6602489780"}, {"first_name"=>"Mark D.", "last_name"=>"Biggin", "scopus_author_id"=>"7004823673"}, {"first_name"=>"Michael B.", "last_name"=>"Eisen", "scopus_author_id"=>"7004331829"}], "year"=>2010, "source"=>"PLoS Biology", "identifiers"=>{"scopus"=>"2-s2.0-77950566643", "doi"=>"10.1371/journal.pbio.1000343", "sgr"=>"77950566643", "isbn"=>"10.1371/journal.pbio.1000343", "pmid"=>"20351773", "issn"=>"15449173", "pui"=>"358592367"}, "id"=>"fcf3e183-044c-3561-bc99-5fe5ef259e74", "abstract"=>"Changes in gene expression play an important role in evolution, yet the molecular mechanisms underlying regulatory evolution are poorly understood. Here we compare genome-wide binding of the six transcription factors that initiate segmentation along the anterior-posterior axis in embryos of two closely related species: Drosophila melanogaster and Drosophila yakuba. Where we observe binding by a factor in one species, we almost always observe binding by that factor to the orthologous sequence in the other species. Levels of binding, however, vary considerably. The magnitude and direction of the interspecies differences in binding levels of all six factors are strongly correlated, suggesting a role for chromatin or other factor-independent forces in mediating the divergence of transcription factor binding. Nonetheless, factor-specific quantitative variation in binding is common, and we show that it is driven to a large extent by the gain and loss of cognate recognition sequences for the given factor. We find only a weak correlation between binding variation and regulatory function. These data provide the first genome-wide picture of how modest levels of sequence divergence between highly morphologically similar species affect a system of coordinately acting transcription factors during animal development, and highlight the dominant role of quantitative variation in transcription factor binding over short evolutionary distances.", "link"=>"http://www.mendeley.com/research/binding-site-turnover-produces-pervasive-quantitative-changes-transcription-factor-binding-between-c", "reader_count"=>240, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>27, "Researcher"=>73, "Student > Doctoral Student"=>13, "Student > Ph. D. Student"=>70, "Student > Postgraduate"=>6, "Student > Master"=>16, "Other"=>7, "Student > Bachelor"=>6, "Lecturer"=>2, "Professor"=>20}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>27, "Researcher"=>73, "Student > Doctoral Student"=>13, "Student > Ph. D. Student"=>70, "Student > Postgraduate"=>6, "Student > Master"=>16, "Other"=>7, "Student > Bachelor"=>6, "Lecturer"=>2, "Professor"=>20}, "reader_count_by_subject_area"=>{"Engineering"=>3, "Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>31, "Materials Science"=>1, "Mathematics"=>1, "Agricultural and Biological Sciences"=>186, "Medicine and Dentistry"=>5, "Neuroscience"=>3, "Sports and Recreations"=>1, "Physics and Astronomy"=>1, "Social Sciences"=>1, "Computer Science"=>6}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>5}, "Neuroscience"=>{"Neuroscience"=>3}, "Social Sciences"=>{"Social Sciences"=>1}, "Sports and Recreations"=>{"Sports and Recreations"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>186}, "Computer Science"=>{"Computer Science"=>6}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>31}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"United States"=>25, "United Kingdom"=>5, "Switzerland"=>1, "Spain"=>2, "Austria"=>1, "Netherlands"=>1, "Brazil"=>3, "Mexico"=>1, "France"=>5, "Chile"=>2, "Germany"=>2, "Croatia"=>1, "Indonesia"=>1}, "group_count"=>9}

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  • {"files"=>["https://ndownloader.figshare.com/files/426883", "https://ndownloader.figshare.com/files/426988", "https://ndownloader.figshare.com/files/427090", "https://ndownloader.figshare.com/files/427158", "https://ndownloader.figshare.com/files/427263", "https://ndownloader.figshare.com/files/427314", "https://ndownloader.figshare.com/files/427449", "https://ndownloader.figshare.com/files/427564", "https://ndownloader.figshare.com/files/427680", "https://ndownloader.figshare.com/files/427793", "https://ndownloader.figshare.com/files/427882", "https://ndownloader.figshare.com/files/427972", "https://ndownloader.figshare.com/files/428008", "https://ndownloader.figshare.com/files/428134", "https://ndownloader.figshare.com/files/428168", "https://ndownloader.figshare.com/files/428444", "https://ndownloader.figshare.com/files/428470", "https://ndownloader.figshare.com/files/428723", "https://ndownloader.figshare.com/files/428751", "https://ndownloader.figshare.com/files/428985", "https://ndownloader.figshare.com/files/429042", "https://ndownloader.figshare.com/files/429190", "https://ndownloader.figshare.com/files/429240", "https://ndownloader.figshare.com/files/429555", "https://ndownloader.figshare.com/files/429605", "https://ndownloader.figshare.com/files/430143", "https://ndownloader.figshare.com/files/430183", "https://ndownloader.figshare.com/files/430381", "https://ndownloader.figshare.com/files/430512", "https://ndownloader.figshare.com/files/430646", "https://ndownloader.figshare.com/files/430824", "https://ndownloader.figshare.com/files/430965", "https://ndownloader.figshare.com/files/431080", "https://ndownloader.figshare.com/files/431300"], "description"=>"<div><p>Changes in gene expression play an important role in evolution, yet the molecular mechanisms underlying regulatory evolution are poorly understood. Here we compare genome-wide binding of the six transcription factors that initiate segmentation along the anterior-posterior axis in embryos of two closely related species: <em>Drosophila melanogaster</em> and <em>Drosophila yakuba</em>. Where we observe binding by a factor in one species, we almost always observe binding by that factor to the orthologous sequence in the other species. Levels of binding, however, vary considerably. The magnitude and direction of the interspecies differences in binding levels of all six factors are strongly correlated, suggesting a role for chromatin or other factor-independent forces in mediating the divergence of transcription factor binding. Nonetheless, factor-specific quantitative variation in binding is common, and we show that it is driven to a large extent by the gain and loss of cognate recognition sequences for the given factor. We find only a weak correlation between binding variation and regulatory function. These data provide the first genome-wide picture of how modest levels of sequence divergence between highly morphologically similar species affect a system of coordinately acting transcription factors during animal development, and highlight the dominant role of quantitative variation in transcription factor binding over short evolutionary distances.</p></div>", "links"=>[], "tags"=>["binding", "turnover", "produces", "pervasive", "quantitative", "changes", "transcription"], "article_id"=>144267, "categories"=>["Medicine", "Developmental Biology", "Genetics", "Cancer"], "users"=>["Robert K. Bradley", "Xiao-Yong Li", "Cole Trapnell", "Stuart Davidson", "Lior Pachter", "Hou Cheng Chu", "Leath A. Tonkin", "Mark D. Biggin", "Michael B. Eisen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000343.s001", "https://dx.doi.org/10.1371/journal.pbio.1000343.s002", "https://dx.doi.org/10.1371/journal.pbio.1000343.s003", "https://dx.doi.org/10.1371/journal.pbio.1000343.s004", "https://dx.doi.org/10.1371/journal.pbio.1000343.s005", "https://dx.doi.org/10.1371/journal.pbio.1000343.s006", "https://dx.doi.org/10.1371/journal.pbio.1000343.s007", "https://dx.doi.org/10.1371/journal.pbio.1000343.s008", "https://dx.doi.org/10.1371/journal.pbio.1000343.s009", "https://dx.doi.org/10.1371/journal.pbio.1000343.s010", "https://dx.doi.org/10.1371/journal.pbio.1000343.s011", "https://dx.doi.org/10.1371/journal.pbio.1000343.s012", "https://dx.doi.org/10.1371/journal.pbio.1000343.s013", "https://dx.doi.org/10.1371/journal.pbio.1000343.s014", "https://dx.doi.org/10.1371/journal.pbio.1000343.s015", "https://dx.doi.org/10.1371/journal.pbio.1000343.s016", "https://dx.doi.org/10.1371/journal.pbio.1000343.s017", "https://dx.doi.org/10.1371/journal.pbio.1000343.s018", "https://dx.doi.org/10.1371/journal.pbio.1000343.s019", "https://dx.doi.org/10.1371/journal.pbio.1000343.s020", "https://dx.doi.org/10.1371/journal.pbio.1000343.s021", "https://dx.doi.org/10.1371/journal.pbio.1000343.s022", "https://dx.doi.org/10.1371/journal.pbio.1000343.s023", "https://dx.doi.org/10.1371/journal.pbio.1000343.s024", "https://dx.doi.org/10.1371/journal.pbio.1000343.s025", "https://dx.doi.org/10.1371/journal.pbio.1000343.s026", "https://dx.doi.org/10.1371/journal.pbio.1000343.s027", "https://dx.doi.org/10.1371/journal.pbio.1000343.s028", "https://dx.doi.org/10.1371/journal.pbio.1000343.s029", "https://dx.doi.org/10.1371/journal.pbio.1000343.s030", "https://dx.doi.org/10.1371/journal.pbio.1000343.s031", "https://dx.doi.org/10.1371/journal.pbio.1000343.s032", "https://dx.doi.org/10.1371/journal.pbio.1000343.s033", "https://dx.doi.org/10.1371/journal.pbio.1000343.s034"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Binding_Site_Turnover_Produces_Pervasive_Quantitative_Changes_in_Transcription_Factor_Binding_between_Closely_Related_Drosophila_Species/144267", "title"=>"Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related <em>Drosophila</em> Species", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-03-23 01:11:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/857534"], "description"=>"<p>Representative loci showing (A) broad conservation of binding, (B) complete gain and loss of binding peaks, (C) shifts in binding site location, and (D) changes in peak strength with peak location preserved. The line plots show binding to orthologous sequences in <i>D. melanogaster</i> (red) and <i>D. yakuba</i> (green), along with gene models and known regulatory elements in <i>D. melanogaster</i> (top track), where the binding signal is the inferred fragment density. Gaps in the black lines (top two tracks) for each species indicate gaps in the pairwise alignment of the two genomes. The plots are in alignment coordinates, and the chromosome positions indicated with tick marks are sequence coordinates in <i>D. melanogaster</i> (FlyBase release 5). Levels of binding were scaled for each factor and panel as appropriate for display and cannot be compared between factors or panels.</p>", "links"=>[], "tags"=>["computational biology/comparative sequence analysis", "computational biology/evolutionary modeling", "computational biology/genomics", "developmental biology/developmental evolution", "genetics and genomics/comparative genomics", "genetics and genomics/functional genomics"], "article_id"=>527979, "categories"=>["Medicine", "Developmental Biology", "Genetics", "Infectious Diseases"], "users"=>["Robert K. Bradley", "Xiao-Yong Li", "Cole Trapnell", "Stuart Davidson", "Lior Pachter", "Hou Cheng Chu", "Leath A. Tonkin", "Mark D. Biggin", "Michael B. Eisen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000343.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Modes_of_cis_regulatory_conservation_and_divergence_/527979", "title"=>"Modes of <i>cis</i>-regulatory conservation and divergence.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-03-23 02:12:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/857689"], "description"=>"<p>Comparison of binding levels in <i>D. melanogaster</i> and <i>D. yakuba</i> for all identified bound regions. For each peak called in either species, we plotted the corresponding binding strengths in red for <i>D. melanogaster</i> and green for <i>D. yakuba</i>; dark colors indicate peaks near known targets of A-P regulation. Peaks are ordered left-to-right on the <i>x</i>-axis according to their binding ranks in <i>D. melanogaster</i>, and binding strengths in both genomes are plotted in log scale on the <i>y</i>-axis (binding units are arbitrary). Binding strength is well-conserved for both peaks within 10 Kb of the 5′ end of genes known to be regulated by A-P factors (“<i>r</i><sub>A-P</sub>”) and those that are not (“<i>r</i>”) (list of A-P target genes given in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000343#s4\" target=\"_blank\">Methods</a>).</p>", "links"=>[], "tags"=>["binding"], "article_id"=>528142, "categories"=>["Medicine", "Developmental Biology", "Genetics", "Infectious Diseases"], "users"=>["Robert K. Bradley", "Xiao-Yong Li", "Cole Trapnell", "Stuart Davidson", "Lior Pachter", "Hou Cheng Chu", "Leath A. Tonkin", "Mark D. Biggin", "Michael B. Eisen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000343.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Quantitative_variation_in_binding_between_species_/528142", "title"=>"Quantitative variation in binding between species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-03-23 02:15:42"}
  • {"files"=>["https://ndownloader.figshare.com/files/857962"], "description"=>"<p>Comparison of the fractional binding divergence, computed as |<i>D. melanogaster</i> − <i>D. yakuba</i>| / (<i>D. melanogaster</i> + <i>D. yakuba</i>), with total levels of binding. Each plotted point corresponds to the median fractional binding divergence for overlapping cohorts of 250 peaks, and the error bars show the standard deviation of the fractional binding divergence within these cohorts. Note that the sharp increases at the right-hand sides of the plots correspond to peaks that are present in <i>D. yakuba</i> but not in <i>D. melanogaster</i>. <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000343#pbio.1000343.s007\" target=\"_blank\">Figure S7</a> shows the same data but displays the fractional binding divergence for every peak rather than binning by cohort (as here).</p>", "links"=>[], "tags"=>["binding", "divergence"], "article_id"=>528413, "categories"=>["Medicine", "Developmental Biology", "Genetics", "Infectious Diseases"], "users"=>["Robert K. Bradley", "Xiao-Yong Li", "Cole Trapnell", "Stuart Davidson", "Lior Pachter", "Hou Cheng Chu", "Leath A. Tonkin", "Mark D. Biggin", "Michael B. Eisen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000343.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fractional_binding_divergence_is_largely_independent_of_binding_strength_/528413", "title"=>"Fractional binding divergence is largely independent of binding strength.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-03-23 02:20:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/858251"], "description"=>"<p>We identified a total of 26 divergence-driving words (7 bp) for BCD (1), HB (12), KR (10), and GT (3). A red box in a (row, column) entry indicates that the corresponding word (row) was identified as a DDW for a particular factor (column); similarly, a solid circle in a (row, column) indicates that a word (row) matches the DNA-binding specificity of a factor analyzed here (column), and an empty circle in a (row, column) indicates that a word (row) identified as a DDW for a particular factor (column) matches the specificity of an A-P transcription factor (plus Zelda), other than the six analyzed here, as characterized by <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000343#pbio.1000343-Noyes1\" target=\"_blank\">[29]</a>. Sequence motifs and their reverse complements are shown in the row labels.</p>", "links"=>[], "tags"=>["driven", "turnover", "transcription", "binding"], "article_id"=>528699, "categories"=>["Medicine", "Developmental Biology", "Genetics", "Infectious Diseases"], "users"=>["Robert K. Bradley", "Xiao-Yong Li", "Cole Trapnell", "Stuart Davidson", "Lior Pachter", "Hou Cheng Chu", "Leath A. Tonkin", "Mark D. Biggin", "Michael B. Eisen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000343.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Divergence_is_driven_by_turnover_of_transcription_factor_binding_sites_/528699", "title"=>"Divergence is driven by turnover of transcription factor binding sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-03-23 02:24:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/858755"], "description"=>"<p>With the exception of BCD, we observed only a weak relationship between binding strength and enrichment (red) and conservation (yellow) of motifs identified for single factors, despite our expectation that strongly bound regions would be subject to greater functional constraint. The fraction of peaks containing one or more DDWs in <i>D. melanogaster</i> (red circles) decreased quickly with binding strength for BCD only, and was consistently higher than the background across the genome (red dashed line) for all factors. Notably, the fraction of these motifs that were conserved between <i>D. melanogaster</i> and <i>D. yakuba</i> (orange triangles) was largely independent of binding strength, and was consistently higher than the background levels of conservation of these motifs across the genome (orange dashed line). Motif enrichment (6 bp DDWs) in <i>D. melanogaster</i> and conservation in the two genomes were calculated for overlapping cohorts of 250 peaks.</p>", "links"=>[], "tags"=>["divergence-driving"], "article_id"=>529208, "categories"=>["Medicine", "Developmental Biology", "Genetics", "Infectious Diseases"], "users"=>["Robert K. Bradley", "Xiao-Yong Li", "Cole Trapnell", "Stuart Davidson", "Lior Pachter", "Hou Cheng Chu", "Leath A. Tonkin", "Mark D. Biggin", "Michael B. Eisen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000343.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enrichment_and_conservation_of_divergence_driving_words_/529208", "title"=>"Enrichment and conservation of divergence-driving words.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-03-23 02:33:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/859168"], "description"=>"<p>PCA of (A) the relative change in binding strength across all peaks, and the binding in (B) <i>D. melanogaster</i> and (C) <i>D. yakuba</i>. Each row represents a factor, and each column is a principal component of the relevant data. The color represents the sign (red positive, green negative) and magnitude (color intensity) of each value in each principal component vector. Note that in each case the sign of the first principal component is the same for all six factors, indicating that the dominant driver of both interspecies divergence and quantitative variation within single species is a coordinated change in binding strength of all factors. This effect, which could be due to changes in chromatin state, explained 38% of the variation between species, and 62% (<i>D. melanogaster</i>) and 55% (<i>D. yakuba</i>) of the variation within species.</p>", "links"=>[], "tags"=>["binding"], "article_id"=>529619, "categories"=>["Medicine", "Developmental Biology", "Genetics", "Infectious Diseases"], "users"=>["Robert K. Bradley", "Xiao-Yong Li", "Cole Trapnell", "Stuart Davidson", "Lior Pachter", "Hou Cheng Chu", "Leath A. Tonkin", "Mark D. Biggin", "Michael B. Eisen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000343.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principal_component_analysis_of_binding_of_all_factors_/529619", "title"=>"Principal component analysis of binding of all factors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-03-23 02:40:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/859582"], "description"=>"<p>We identified divergence-driving words for each of the principal components in <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000343#pbio-1000343-g006\" target=\"_blank\">Figure 6A</a>. Few words are shared by the different principal components, suggesting that distinct sets of motifs and A-P regulators govern the different patterns of variation revealed by PCA. The CAGGTAG binding site for the early zygotic activator Zelda drives divergence of coherent binding of all factors (principal component 1). A red box in a (row, column) entry indicates that the corresponding word (row) was identified as a DDW for a particular principal component (column); a solid circle in a (row, column) indicates that a word (row) matches the DNA-binding specificity of a factor analyzed here, plus Zelda (column). In contrast to <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000343#pbio-1000343-g004\" target=\"_blank\">Figure 4</a>, where empty circles are used to indicate matches to A-P factors other than the six analyzed here, no empty circles are shown here because all words match the specificities of one or more additional A-P regulators, as characterized by <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000343#pbio.1000343-Noyes1\" target=\"_blank\">[29]</a>. Sequence motifs and their reverse complements are shown in the row labels.</p>", "links"=>[], "tags"=>["words"], "article_id"=>530031, "categories"=>["Medicine", "Developmental Biology", "Genetics", "Infectious Diseases"], "users"=>["Robert K. Bradley", "Xiao-Yong Li", "Cole Trapnell", "Stuart Davidson", "Lior Pachter", "Hou Cheng Chu", "Leath A. Tonkin", "Mark D. Biggin", "Michael B. Eisen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000343.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Divergence_driving_words_for_principal_components_/530031", "title"=>"Divergence-driving words for principal components.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-03-23 00:00:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/859691"], "description"=>"<p>We required that sequenced tags map uniquely to the genome with at most one mismatch. The Input controls were segregated based on the average fragment length (225 or 250 bp); identical fragment lengths were used in both species for particular antibodies.</p>", "links"=>[], "tags"=>["computational biology/comparative sequence analysis", "computational biology/evolutionary modeling", "computational biology/genomics", "developmental biology/developmental evolution", "genetics and genomics/comparative genomics", "genetics and genomics/functional genomics"], "article_id"=>530142, "categories"=>["Medicine", "Developmental Biology", "Genetics", "Infectious Diseases"], "users"=>["Robert K. Bradley", "Xiao-Yong Li", "Cole Trapnell", "Stuart Davidson", "Lior Pachter", "Hou Cheng Chu", "Leath A. Tonkin", "Mark D. Biggin", "Michael B. Eisen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000343.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Sequencing_and_mapping_statistics_/530142", "title"=>"Sequencing and mapping statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-03-23 00:02:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/859733"], "description"=>"<p>Peaks were called as absent if the binding signal was reduced 10-fold or more in its ortholog. The denominators include only peaks where orthologs could be identified.</p>", "links"=>[], "tags"=>["computational biology/comparative sequence analysis", "computational biology/evolutionary modeling", "computational biology/genomics", "developmental biology/developmental evolution", "genetics and genomics/comparative genomics", "genetics and genomics/functional genomics"], "article_id"=>530178, "categories"=>["Medicine", "Developmental Biology", "Genetics", "Infectious Diseases"], "users"=>["Robert K. Bradley", "Xiao-Yong Li", "Cole Trapnell", "Stuart Davidson", "Lior Pachter", "Hou Cheng Chu", "Leath A. Tonkin", "Mark D. Biggin", "Michael B. Eisen"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000343.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gain_and_loss_of_peaks_/530178", "title"=>"Gain and loss of peaks.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-03-23 00:02:58"}

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Relative Metric

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