Genome-Wide Analysis of Alternative Splicing during Dendritic Cell Response to a Bacterial Challenge
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{"title"=>"Genome-Wide Analysis of Alternative Splicing during Dendritic Cell Response to a Bacterial Challenge", "type"=>"journal", "authors"=>[{"first_name"=>"Raquel", "last_name"=>"Rodrigues", "scopus_author_id"=>"39862203700"}, {"first_name"=>"Ana Rita", "last_name"=>"Grosso", "scopus_author_id"=>"26639262500"}, {"first_name"=>"Luís", "last_name"=>"Moita", "scopus_author_id"=>"8638960300"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84876265387", "pmid"=>"23613991", "sgr"=>"84876265387", "issn"=>"19326203", "pui"=>"368743333", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0061975"}, "id"=>"05db5eae-9f22-3f29-bc97-4a262225334a", "abstract"=>"The immune system relies on the plasticity of its components to produce appropriate responses to frequent environmental challenges. Dendritic cells (DCs) are critical initiators of innate immunity and orchestrate the later and more specific adaptive immunity. The generation of diversity in transcriptional programs is central for effective immune responses. Alternative splicing is widely considered a key generator of transcriptional and proteomic complexity, but its role has been rarely addressed systematically in immune cells. Here we used splicing-sensitive arrays to assess genome-wide gene- and exon-level expression profiles in human DCs in response to a bacterial challenge. We find widespread alternative splicing events and splicing factor transcriptional signatures induced by an E. coli challenge to human DCs. Alternative splicing acts in concert with transcriptional modulation, but these two mechanisms of gene regulation affect primarily distinct functional gene groups. Alternative splicing is likely to have an important role in DC immunobiology because it affects genes known to be involved in DC development, endocytosis, antigen presentation and cell cycle arrest.", "link"=>"http://www.mendeley.com/research/genomewide-analysis-alternative-splicing-during-dendritic-cell-response-bacterial-challenge-1", "reader_count"=>21, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>5, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>5, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>5, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>10, "Medicine and Dentistry"=>4, "Social Sciences"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Germany"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1027297"], "description"=>"<p>Dynamic heatmap (T1, T2 and T3) of the 30 functional groups obtained by grouping the related terms within enriched gene sets in alternatively spliced genes (yellow), differentially expressed genes (blue) or both (green). Details are provided in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061975#pone.0061975.s010\" target=\"_blank\">Table S9</a>.</p>", "links"=>[], "tags"=>["immunology", "Immune cells", "Antigen-presenting cells", "immunity", "Adaptive immunity", "Immune defense", "Immunity to infections", "Innate immunity", "Immune response", "microbiology", "Bacterial pathogens", "Escherichia coli", "Molecular cell biology", "Nucleic acids", "rna", "RNA processing", "systems biology", "Anatomy and physiology", "Immune physiology", "Clinical immunology", "Infectious diseases", "Bacterial diseases", "differentially", "alternatively", "spliced"], "article_id"=>684731, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Raquel Rodrigues", "Ana Rita Grosso", "Luís Moita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061975.g006", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functional_Analysis_of_differentially_expressed_and_alternatively_spliced_genes_/684731", "title"=>"Functional Analysis of differentially expressed and alternatively spliced genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-17 01:18:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/1027311", "https://ndownloader.figshare.com/files/1027313", "https://ndownloader.figshare.com/files/1027315", "https://ndownloader.figshare.com/files/1027316", "https://ndownloader.figshare.com/files/1027317", "https://ndownloader.figshare.com/files/1027318", "https://ndownloader.figshare.com/files/1027319", "https://ndownloader.figshare.com/files/1027320", "https://ndownloader.figshare.com/files/1027326", "https://ndownloader.figshare.com/files/1027327"], "description"=>"<div><p>The immune system relies on the plasticity of its components to produce appropriate responses to frequent environmental challenges. Dendritic cells (DCs) are critical initiators of innate immunity and orchestrate the later and more specific adaptive immunity. The generation of diversity in transcriptional programs is central for effective immune responses. Alternative splicing is widely considered a key generator of transcriptional and proteomic complexity, but its role has been rarely addressed systematically in immune cells. Here we used splicing-sensitive arrays to assess genome-wide gene- and exon-level expression profiles in human DCs in response to a bacterial challenge. We find widespread alternative splicing events and splicing factor transcriptional signatures induced by an <i>E. coli</i> challenge to human DCs. Alternative splicing acts in concert with transcriptional modulation, but these two mechanisms of gene regulation affect primarily distinct functional gene groups. Alternative splicing is likely to have an important role in DC immunobiology because it affects genes known to be involved in DC development, endocytosis, antigen presentation and cell cycle arrest.</p> </div>", "links"=>[], "tags"=>["immunology", "Immune cells", "Antigen-presenting cells", "immunity", "Adaptive immunity", "Immune defense", "Immunity to infections", "Innate immunity", "Immune response", "microbiology", "Bacterial pathogens", "Escherichia coli", "Molecular cell biology", "Nucleic acids", "rna", "RNA processing", "systems biology", "Anatomy and physiology", "Immune physiology", "Clinical immunology", "Infectious diseases", "Bacterial diseases", "splicing", "dendritic", "bacterial"], "article_id"=>684745, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Raquel Rodrigues", "Ana Rita Grosso", "Luís Moita"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0061975.s001", "https://dx.doi.org/10.1371/journal.pone.0061975.s002", "https://dx.doi.org/10.1371/journal.pone.0061975.s003", "https://dx.doi.org/10.1371/journal.pone.0061975.s004", "https://dx.doi.org/10.1371/journal.pone.0061975.s005", "https://dx.doi.org/10.1371/journal.pone.0061975.s006", "https://dx.doi.org/10.1371/journal.pone.0061975.s007", "https://dx.doi.org/10.1371/journal.pone.0061975.s008", "https://dx.doi.org/10.1371/journal.pone.0061975.s009", "https://dx.doi.org/10.1371/journal.pone.0061975.s010"], "stats"=>{"downloads"=>26, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genome_Wide_Analysis_of_Alternative_Splicing_during_Dendritic_Cell_Response_to_a_Bacterial_Challenge_/684745", "title"=>"Genome-Wide Analysis of Alternative Splicing during Dendritic Cell Response to a Bacterial Challenge", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-04-17 01:19:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/1027296"], "description"=>"<p>Analysis of PCR products on GelRed stained 1.5–2% agarose gels (in some cases the figure was cropped so that the lane with the DNA ladder was adjacent to the lanes of interest) and schematic representation of the region of the gene that was tested. The yellow asterisk marks the significant probeset and the blue boxes represent the areas where the primers were designed to anneal. The same amount of cDNA was used in all RT-PCR reactions, as shown in GAPDH amplification reaction. Details are supplied in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061975#pone.0061975.s003\" target=\"_blank\">Table S2</a>.</p>", "links"=>[], "tags"=>["immunology", "Immune cells", "Antigen-presenting cells", "immunity", "Adaptive immunity", "Immune defense", "Immunity to infections", "Innate immunity", "Immune response", "microbiology", "Bacterial pathogens", "Escherichia coli", "Molecular cell biology", "Nucleic acids", "rna", "RNA processing", "systems biology", "Anatomy and physiology", "Immune physiology", "Clinical immunology", "Infectious diseases", "Bacterial diseases", "validated", "genes", "splicing", "dendritic", "cells"], "article_id"=>684730, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Raquel Rodrigues", "Ana Rita Grosso", "Luís Moita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061975.g005", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Positively_validated_genes_with_alternative_splicing_in_dendritic_cells_after_challenge_with_E_coli_/684730", "title"=>"Positively validated genes with alternative splicing in dendritic cells after challenge with <i>E.coli</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-17 01:18:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/1027291"], "description"=>"<p>Venn diagrams of differentially expressed genes and alternative splicing events after (e) 4 h, (f) 8 h and (g) 18 h of stimulus. (in blue: percentage of the differentially expressed genes that are also alternatively spliced; in pink: percentage of the alternatively spliced genes that are also differentially expressed).</p>", "links"=>[], "tags"=>["immunology", "Immune cells", "Antigen-presenting cells", "immunity", "Adaptive immunity", "Immune defense", "Immunity to infections", "Innate immunity", "Immune response", "microbiology", "Bacterial pathogens", "Escherichia coli", "Molecular cell biology", "Nucleic acids", "rna", "RNA processing", "systems biology", "Anatomy and physiology", "Immune physiology", "Clinical immunology", "Infectious diseases", "Bacterial diseases", "diagrams", "differentially", "splicing", "alternatively", "spliced", "genes", "dendritic", "exon", "evaluated", "t1", "t2", "t3"], "article_id"=>684725, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Raquel Rodrigues", "Ana Rita Grosso", "Luís Moita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061975.g001", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Venn_diagrams_of_the_a_differentially_expressed_genes_b_differentially_expressed_splicing_factors_c_alternatively_spliced_genes_and_d_alternative_splicing_events_in_dendritic_cells_according_to_exon_array_analysis_following_E_coli_challenge_in_the_evalua/684725", "title"=>"Venn diagrams of the (a) differentially expressed genes, (b) differentially expressed splicing factors, (c) alternatively spliced genes and (d) alternative splicing events in dendritic cells, according to exon array analysis, following <i>E.coli</i> challenge in the evaluated timepoints: T1 (4 h), T2 (8 h), T3 (18 h).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-17 01:18:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/1027298"], "description"=>"<p>AS – alternative splicing, Up – upregulated, Down – downregulated.</p>", "links"=>[], "tags"=>["immunology", "Immune cells", "Antigen-presenting cells", "immunity", "Adaptive immunity", "Immune defense", "Immunity to infections", "Innate immunity", "Immune response", "microbiology", "Bacterial pathogens", "Escherichia coli", "Molecular cell biology", "Nucleic acids", "rna", "RNA processing", "systems biology", "Anatomy and physiology", "Immune physiology", "Clinical immunology", "Infectious diseases", "Bacterial diseases", "genes", "splicing", "appraised"], "article_id"=>684732, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Raquel Rodrigues", "Ana Rita Grosso", "Luís Moita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061975.t001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differentially_Expressed_Genes_and_Alternative_Splicing_in_DCs_upon_E_coli_challenge_in_the_three_appraised_timepoints_/684732", "title"=>"Differentially Expressed Genes and Alternative Splicing in DCs, upon <i>E.coli</i> challenge in the three appraised timepoints.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-04-17 01:18:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/1027293"], "description"=>"<p>(<b>a</b>) Overall trends of expression of the splicing factors (<b>b</b>) Trends of expression of the splicing factors across the analyzed timepoints: T1 (4 h), T2 (8 h), T3 (18 h) – percentage of the up and downregulated splicing factors.</p>", "links"=>[], "tags"=>["immunology", "Immune cells", "Antigen-presenting cells", "immunity", "Adaptive immunity", "Immune defense", "Immunity to infections", "Innate immunity", "Immune response", "microbiology", "Bacterial pathogens", "Escherichia coli", "Molecular cell biology", "Nucleic acids", "rna", "RNA processing", "systems biology", "Anatomy and physiology", "Immune physiology", "Clinical immunology", "Infectious diseases", "Bacterial diseases", "splicing"], "article_id"=>684727, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Raquel Rodrigues", "Ana Rita Grosso", "Luís Moita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061975.g003", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differentially_expressed_splicing_factors_/684727", "title"=>"Differentially expressed splicing factors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-17 01:18:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/1027294"], "description"=>"<p>(<b>a</b>) Protein family distribution of the differentially expressed splicing factors; (<b>b</b>) Heatmap with the fold changes (log(2)) observed for the differentially expressed splicing factors, at the three evaluated timepoints (T1: 4 h; T2: 8 h; T3: 18 h), grouped by protein family. The genes and respective logfold changes are presented in detail in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061975#pone.0061975.s007\" target=\"_blank\">Table S6</a>.</p>", "links"=>[], "tags"=>["immunology", "Immune cells", "Antigen-presenting cells", "immunity", "Adaptive immunity", "Immune defense", "Immunity to infections", "Innate immunity", "Immune response", "microbiology", "Bacterial pathogens", "Escherichia coli", "Molecular cell biology", "Nucleic acids", "rna", "RNA processing", "systems biology", "Anatomy and physiology", "Immune physiology", "Clinical immunology", "Infectious diseases", "Bacterial diseases", "differentially", "splicing"], "article_id"=>684728, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Raquel Rodrigues", "Ana Rita Grosso", "Luís Moita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061975.g004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Protein_families_of_the_differentially_expressed_splicing_factors_/684728", "title"=>"Protein families of the differentially expressed splicing factors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-17 01:18:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/1027292"], "description"=>"<p>Twenty-eight differentially expressed genes, according to array analysis, were tested by qPCR in dendritic cells, comparing non-stimulated and challenged cells. Results are presented in log(2). (See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061975#pone.0061975.s002\" target=\"_blank\">Table S1</a> for details).</p>", "links"=>[], "tags"=>["immunology", "Immune cells", "Antigen-presenting cells", "immunity", "Adaptive immunity", "Immune defense", "Immunity to infections", "Innate immunity", "Immune response", "microbiology", "Bacterial pathogens", "Escherichia coli", "Molecular cell biology", "Nucleic acids", "rna", "RNA processing", "systems biology", "Anatomy and physiology", "Immune physiology", "Clinical immunology", "Infectious diseases", "Bacterial diseases", "quantitative", "Real-time", "polymerase"], "article_id"=>684726, "categories"=>["Medicine", "Biological Sciences"], "users"=>["Raquel Rodrigues", "Ana Rita Grosso", "Luís Moita"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0061975.g002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Validation_of_array_results_by_quantitative_real_time_polymerase_chain_reaction_/684726", "title"=>"Validation of array results by quantitative real-time polymerase chain reaction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-17 01:18:46"}

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  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"8", "full-text"=>"7", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[269, 466, 588, 697, 800, 896, 988, 1076, 1165, 1254, 1340, 1417]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[266, 468, 593, 703, 804, 903, 993, 1084, 1171, 1256, 1339, 1422, 1492]}, {"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[284, 491, 620, 738, 843, 945, 1043, 1137, 1225, 1315, 1400, 1479, 1555]}, {"subject_area"=>"/Biology and life sciences/Immunology", "average_usage"=>[266, 466, 591, 701, 799, 887, 982, 1067, 1155, 1237, 1317, 1395, 1458]}, {"subject_area"=>"/Medicine and health sciences/Immunology", "average_usage"=>[262, 463, 587, 693, 790, 882, 965, 1051, 1135, 1218, 1300, 1376, 1438]}]}
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