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{"title"=>"A Comparative Analysis of Transcription Factor Expression during Metazoan Embryonic Development", "type"=>"journal", "authors"=>[{"first_name"=>"Alicia N.", "last_name"=>"Schep", "scopus_author_id"=>"36462711400"}, {"first_name"=>"Boris", "last_name"=>"Adryan", "scopus_author_id"=>"15057657300"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84879173032", "doi"=>"10.1371/journal.pone.0066826", "pui"=>"369140297", "pmid"=>"23799133", "scopus"=>"2-s2.0-84879173032", "issn"=>"19326203", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"d1952907-a787-3d1b-bb09-dec47007947b", "abstract"=>"During embryonic development, a complex organism is formed from a single starting cell. These processes of growth and differentiation are driven by large transcriptional changes, which are following the expression and activity of transcription factors (TFs). This study sought to compare TF expression during embryonic development in a diverse group of metazoan animals: representatives of vertebrates (Danio rerio, Xenopus tropicalis), a chordate (Ciona intestinalis) and invertebrate phyla such as insects (Drosophila melanogaster, Anopheles gambiae) and nematodes (Caenorhabditis elegans) were sampled, The different species showed overall very similar TF expression patterns, with TF expression increasing during the initial stages of development. C2H2 zinc finger TFs were over-represented and Homeobox TFs were under-represented in the early stages in all species. We further clustered TFs for each species based on their quantitative temporal expression profiles. This showed very similar TF expression trends in development in vertebrate and insect species. However, analysis of the expression of orthologous pairs between more closely related species showed that expression of most individual TFs is not conserved, following the general model of duplication and diversification. The degree of similarity between TF expression between Xenopus tropicalis and Danio rerio followed the hourglass model, with the greatest similarity occuring during the early tailbud stage in Xenopus tropicalis and the late segmentation stage in Danio rerio. However, for Drosophila melanogaster and Anopheles gambiae there were two periods of high TF transcriptome similarity, one during the Arthropod phylotypic stage at 8-10 hours into Drosophila development and the other later at 16-18 hours into Drosophila development.", "link"=>"http://www.mendeley.com/research/comparative-analysis-transcription-factor-expression-during-metazoan-embryonic-development-1", "reader_count"=>45, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>13, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>16, "Student > Master"=>8, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>13, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>16, "Student > Master"=>8, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>36, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>36}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Argentina"=>1, "United States"=>2, "United Kingdom"=>4, "France"=>1, "Spain"=>2, "Russia"=>1}, "group_count"=>2}

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• http://doi.org/10.1016/j.fsi.2014.07.018
• http://doi.org/10.1002/evl3.115
• http://doi.org/10.1093/molbev/msv012
• http://doi.org/10.1111/brv.12117
• http://doi.org/10.1016/j.ydbio.2015.07.003
• http://doi.org/10.1186/s12862-015-0505-z
• http://doi.org/10.1186/s13227-018-0095-0
• http://doi.org/10.1002/jez.b.22569
• http://doi.org/10.1002/mrd.22607
• http://doi.org/10.1093/molbev/msw013
• http://doi.org/10.1186/s12864-016-2839-3
• http://doi.org/10.1093/aob/mcw024
• http://doi.org/10.1002/jcp.27386
• http://doi.org/10.1016/j.mod.2017.02.001
• http://doi.org/10.1016/j.gde.2017.04.004
• http://doi.org/10.1093/gbe/evu030
• http://doi.org/10.1016/j.ydbio.2015.05.014
• http://doi.org/10.1016/j.ygeno.2020.02.004
• http://doi.org/10.12688/f1000research.4583.2

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• {"id"=>"349213524561637376", "text"=>"Schep & Adryan: \"A Comparative Analysis of Transcription Factor Expression during Metazoan Embryonic Development\" out http://t.co/6XN1Q9JEKN", "created_at"=>"2013-06-24T17:12:46Z", "user"=>"BorisAdryan", "user_name"=>"Boris Adryan", "user_profile_image"=>"http://a0.twimg.com/profile_images/2744773916/1738bf480dde7fb2ab0ad7312b87c63e_normal.png"}
• {"id"=>"351262138632904704", "text"=>"Boris @BorisAdryan joins the hourglass bussiness http://t.co/RGd7UY2d8O Congrats on a nice paper comparing TF expression across species.", "created_at"=>"2013-06-30T08:53:14Z", "user"=>"PavelTomancak", "user_name"=>"Pavel Tomancak", "user_profile_image"=>"http://a0.twimg.com/profile_images/2612422002/2jn1eaf2u5v2ampkzd0e_normal.png"}
• {"id"=>"357042133095559169", "text"=>"New hourglass paper focused on transcription factors: http://t.co/29bu5wlW6H (hey, could've cited http://t.co/jnz2a5tAzI, but OK) #evodevo", "created_at"=>"2013-07-16T07:40:52Z", "user"=>"marc_rr", "user_name"=>"Marc RobinsonRechavi", "user_profile_image"=>"http://a0.twimg.com/profile_images/1751744306/mrr_caricature_normal.jpg"}
• {"id"=>"357042792645664769", "text"=>"RT @marc_rr: New hourglass paper focused on transcription factors: http://t.co/29bu5wlW6H (hey, could've cited http://t.co/jnz2a5tAzI, but …", "created_at"=>"2013-07-16T07:43:29Z", "user"=>"amarcobio", "user_name"=>"Antonio Marco", "user_profile_image"=>"http://a0.twimg.com/profile_images/2885948437/25f59d3a1bb09978aaf64f716d7e6749_normal.jpeg"}

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/1088369", "https://ndownloader.figshare.com/files/1088373", "https://ndownloader.figshare.com/files/1088374", "https://ndownloader.figshare.com/files/1088377", "https://ndownloader.figshare.com/files/1088378", "https://ndownloader.figshare.com/files/1088379", "https://ndownloader.figshare.com/files/1088380", "https://ndownloader.figshare.com/files/1088381", "https://ndownloader.figshare.com/files/1088382", "https://ndownloader.figshare.com/files/1088383"], "description"=>"<div><p>During embryonic development, a complex organism is formed from a single starting cell. These processes of growth and differentiation are driven by large transcriptional changes, which are following the expression and activity of transcription factors (TFs). This study sought to compare TF expression during embryonic development in a diverse group of metazoan animals: representatives of vertebrates (<i>Danio rerio</i>, <i>Xenopus tropicalis</i>), a chordate (<i>Ciona intestinalis</i>) and invertebrate phyla such as insects (<i>Drosophila melanogaster</i>, <i>Anopheles gambiae</i>) and nematodes (<i>Caenorhabditis elegans</i>) were sampled, The different species showed overall very similar TF expression patterns, with TF expression increasing during the initial stages of development. C2H2 zinc finger TFs were over-represented and Homeobox TFs were under-represented in the early stages in all species. We further clustered TFs for each species based on their quantitative temporal expression profiles. This showed very similar TF expression trends in development in vertebrate and insect species. However, analysis of the expression of orthologous pairs between more closely related species showed that expression of most individual TFs is not conserved, following the general model of duplication and diversification. The degree of similarity between TF expression between <i>Xenopus tropicalis</i> and <i>Danio rerio</i> followed the hourglass model, with the greatest similarity occuring during the early tailbud stage in <i>Xenopus tropicalis</i> and the late segmentation stage in <i>Danio rerio</i>. However, for <i>Drosophila melanogaster</i> and <i>Anopheles gambiae</i> there were two periods of high TF transcriptome similarity, one during the Arthropod phylotypic stage at 8–10 hours into <i>Drosophila</i> development and the other later at 16–18 hours into <i>Drosophila</i> development.</p></div>", "links"=>[], "tags"=>["developmental biology", "Evolutionary developmental biology", "Organism development", "genetics", "gene expression", "genomics", "Genome expression analysis", "Model organisms", "Animal models", "Caenorhabditis elegans", "Ciona intestinalis", "Drosophila melanogaster", "Xenopus laevis", "zebrafish", "comparative", "transcription", "metazoan", "embryonic"], "article_id"=>721214, "categories"=>["Biological Sciences"], "users"=>["Alicia N. Schep", "Boris Adryan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0066826.s001", "https://dx.doi.org/10.1371/journal.pone.0066826.s002", "https://dx.doi.org/10.1371/journal.pone.0066826.s003", "https://dx.doi.org/10.1371/journal.pone.0066826.s004", "https://dx.doi.org/10.1371/journal.pone.0066826.s005", "https://dx.doi.org/10.1371/journal.pone.0066826.s006", "https://dx.doi.org/10.1371/journal.pone.0066826.s007", "https://dx.doi.org/10.1371/journal.pone.0066826.s008", "https://dx.doi.org/10.1371/journal.pone.0066826.s009", "https://dx.doi.org/10.1371/journal.pone.0066826.s010"], "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Comparative_Analysis_of_Transcription_Factor_Expression_during_Metazoan_Embryonic_Development_/721214", "title"=>"A Comparative Analysis of Transcription Factor Expression during Metazoan Embryonic Development", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-06-14 00:20:14"}
• {"files"=>["https://ndownloader.figshare.com/files/1088346"], "description"=>"<p>The gray vertical line in each plot indicates the onset of gastrulation. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066826#pone.0066826.s005\" target=\"_blank\">Table S2</a> shows the numbers of TFs and members of TF families included in each dataset used for this figure.</p>", "links"=>[], "tags"=>["developmental biology", "Evolutionary developmental biology", "Organism development", "genetics", "gene expression", "genomics", "Genome expression analysis", "Model organisms", "Animal models", "Caenorhabditis elegans", "Ciona intestinalis", "Drosophila melanogaster", "Xenopus laevis", "zebrafish", "tf", "embryogenesis", "microarray", "rna-seq"], "article_id"=>721191, "categories"=>["Biological Sciences"], "users"=>["Alicia N. Schep", "Boris Adryan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0066826.g002", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_TF_and_TF_family_expression_throughout_embryogenesis_based_on_microarray_or_RNA_seq_data_/721191", "title"=>"TF and TF family expression throughout embryogenesis based on microarray or RNA-seq data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-14 00:19:51"}
• {"files"=>["https://ndownloader.figshare.com/files/1088359"], "description"=>"<p>(a) The expression profiles of the cluster pairs. The gray vertical line indicates the onset of gastrulation. The plot in the third column shows the values of the centers of the clusters at each of the common time points. Orange is <i>Drosophila melanogaster</i> and blue is <i>Anopheles gambiae</i>. (b) Dendrogram showing hierarchical clustering of the clusters. (c) TF family representation in each cluster. The dark gray represents <i>Drosophila melanogaster</i> and the light gray <i>Anopheles gambiae</i>. Blue stars signify statistically significant over-representation of a TF family in a cluster pair; red stars signify statistically significant under-representation of a TF family in a cluster pair. (d) Clusters that were not paired.</p>", "links"=>[], "tags"=>["developmental biology", "Evolutionary developmental biology", "Organism development", "genetics", "gene expression", "genomics", "Genome expression analysis", "Model organisms", "Animal models", "Caenorhabditis elegans", "Ciona intestinalis", "Drosophila melanogaster", "Xenopus laevis", "zebrafish", "tf", "clusters"], "article_id"=>721204, "categories"=>["Biological Sciences"], "users"=>["Alicia N. Schep", "Boris Adryan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0066826.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_TF_expression_clusters_for_Drosophila_melanogaster_and_Anopheles_gambiae_/721204", "title"=>"Comparison of TF expression clusters for <i>Drosophila melanogaster</i> and <i>Anopheles gambiae</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-14 00:20:04"}
• {"files"=>["https://ndownloader.figshare.com/files/1088353"], "description"=>"<p>(a) The expression profiles of the cluster pairs. The gray vertical line indicates the onset of gastrulation. The plot in the third column shows the values of the centers of the clusters at each of the common time points. Orange is <i>Xenopus tropicalis</i> and blue is <i>Danio rerio</i>. (b) Dendrogram showing hierarchical clustering of the clusters. (c) TF family representation in each cluster. The dark gray represents <i>Xenopus tropicalis</i> and the light gray <i>Danio rerio</i>. Blue stars signify statistically significant over-representation of a TF family in a cluster pair; red stars signify statistically significant under-representation of a TF family in a cluster pair.</p>", "links"=>[], "tags"=>["developmental biology", "Evolutionary developmental biology", "Organism development", "genetics", "gene expression", "genomics", "Genome expression analysis", "Model organisms", "Animal models", "Caenorhabditis elegans", "Ciona intestinalis", "Drosophila melanogaster", "Xenopus laevis", "zebrafish", "tf", "clusters"], "article_id"=>721198, "categories"=>["Biological Sciences"], "users"=>["Alicia N. Schep", "Boris Adryan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0066826.g004", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_TF_expression_clusters_in_Xenopus_tropicalis_XT_and_Danio_rerio_DR_/721198", "title"=>"Comparison of TF expression clusters in <i>Xenopus tropicalis</i> (XT) and <i>Danio rerio</i> (DR).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-14 00:19:58"}
• {"files"=>["https://ndownloader.figshare.com/files/1088350"], "description"=>"<p>(a) The expression patterns of members of each of the seven clusters determined by Mfuzz. The gray vertical line indicates the onset of gastrulation. (b) The relative representation of different TF families in each cluster. Blue stars signify statistically significant over-representation of a TF family in a cluster; red stars signify statistically significant under-representation of a TF family in a cluster.</p>", "links"=>[], "tags"=>["developmental biology", "Evolutionary developmental biology", "Organism development", "genetics", "gene expression", "genomics", "Genome expression analysis", "Model organisms", "Animal models", "Caenorhabditis elegans", "Ciona intestinalis", "Drosophila melanogaster", "Xenopus laevis", "zebrafish", "transcription", "patterns"], "article_id"=>721195, "categories"=>["Biological Sciences"], "users"=>["Alicia N. Schep", "Boris Adryan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0066826.g003", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clustering_of_transcription_factor_expression_patterns_in_C_elegans_/721195", "title"=>"Clustering of transcription factor expression patterns in <i>C. elegans</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-14 00:19:55"}
• {"files"=>["https://ndownloader.figshare.com/files/1088364"], "description"=>"<p>Heatmaps showing the similarity of the TF transcriptome at all time points for (a) <i>Xenopus tropicalis</i> and <i>Danio rerio</i> and (b) <i>Drosophila melanogaster</i> and <i>Anopheles gambiae</i>. Darker blue/violet shading indicates that the TF trancriptomes for the two species at the given times during development are more similar. The profiles on the right shows the minimum distance between (a) each time piont of <i>Xenopus tropicalis</i> and any time point in <i>Danio rerio</i> and (b) each time point of <i>Drosophila melanogaster</i> and any time point in <i>Anopheles gambiae</i>. In (b), the bracketed time periods for <i>Drosopila</i> are those included in the study by Kalinka et al. (2010) that showed that the time period between 8–10 hours is when the transcriptomes of different <i>Drosophila</i> species are most similar. That time period (indicated by a *) is a local maximum for TF transcriptome similarity between the two insects considered in this study; the 16–18 hour time period for <i>Drosophila melanogaster</i> (indicated by a **) is the time period with the greatest TF transcriptome similarity to <i>Anopheles gambiae</i>.</p>", "links"=>[], "tags"=>["developmental biology", "Evolutionary developmental biology", "Organism development", "genetics", "gene expression", "genomics", "Genome expression analysis", "Model organisms", "Animal models", "Caenorhabditis elegans", "Ciona intestinalis", "Drosophila melanogaster", "Xenopus laevis", "zebrafish", "tf", "transcriptomes"], "article_id"=>721209, "categories"=>["Biological Sciences"], "users"=>["Alicia N. Schep", "Boris Adryan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0066826.g006", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Similarity_of_TF_transcriptomes_between_species_/721209", "title"=>"Similarity of TF transcriptomes between species.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-14 00:20:09"}
• {"files"=>["https://ndownloader.figshare.com/files/1088344"], "description"=>"<p>The gray vertical line in each plot indicates the onset of gastrulation. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066826#pone.0066826.s004\" target=\"_blank\">Table S1</a> shows the numbers of TFs and members of TF families included in each dataset used for this figure.</p>", "links"=>[], "tags"=>["developmental biology", "Evolutionary developmental biology", "Organism development", "genetics", "gene expression", "genomics", "Genome expression analysis", "Model organisms", "Animal models", "Caenorhabditis elegans", "Ciona intestinalis", "Drosophila melanogaster", "Xenopus laevis", "zebrafish", "tf", "embryogenesis", "hybridization"], "article_id"=>721189, "categories"=>["Biological Sciences"], "users"=>["Alicia N. Schep", "Boris Adryan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0066826.g001", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_TF_and_TF_family_expression_through_embryogenesis_based_on_in_situ_hybridization_data_/721189", "title"=>"TF and TF family expression through embryogenesis based on <i>in situ</i> hybridization data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-06-14 00:19:49"}

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Relative Metric

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F1000Prime