Copy Number Variations Burden on miRNA Genes Reveals Layers of Complexities Involved in the Regulation of Pathways and Phenotypic Expression
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{"title"=>"Copy number variations burden on mirna genes reveals layers of complexities involved in the regulation of pathways and phenotypic expression", "type"=>"journal", "authors"=>[{"first_name"=>"Avinash M.", "last_name"=>"Veerappa", "scopus_author_id"=>"55736644600"}, {"first_name"=>"Megha", "last_name"=>"Murthy", "scopus_author_id"=>"55782461500"}, {"first_name"=>"Sangeetha", "last_name"=>"Vishweswaraiah", "scopus_author_id"=>"55386913100"}, {"first_name"=>"Kusuma", "last_name"=>"Lingaiah", "scopus_author_id"=>"55782376800"}, {"first_name"=>"Raviraj V.", "last_name"=>"Suresh", "scopus_author_id"=>"56074400000"}, {"first_name"=>"Somanna Ajjamada", "last_name"=>"Nachappa", "scopus_author_id"=>"56074273600"}, {"first_name"=>"Nelchi", "last_name"=>"Prashali", "scopus_author_id"=>"56075031300"}, {"first_name"=>"Sangeetha Nuggehalli", "last_name"=>"Yadav", "scopus_author_id"=>"56074906300"}, {"first_name"=>"Manjula Arsikere", "last_name"=>"Srikanta", "scopus_author_id"=>"56074315400"}, {"first_name"=>"Dinesh S.", "last_name"=>"Manjegowda", "scopus_author_id"=>"56053307700"}, {"first_name"=>"Keshava B.", "last_name"=>"Seshachalam", "scopus_author_id"=>"56074398100"}, {"first_name"=>"Nallur B.", "last_name"=>"Ramachandra", "scopus_author_id"=>"55917375700"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"372643334", "doi"=>"10.1371/journal.pone.0090391", "pmid"=>"24587348", "issn"=>"19326203", "scopus"=>"2-s2.0-84896509966", "sgr"=>"84896509966"}, "id"=>"2c84c934-a21e-3101-845c-23c224fd4c1c", "abstract"=>"MicroRNAs are involved in post-transcriptional down-regulation of gene expression. Variations in miRNA genes can severely affect downstream-regulated genes and their pathways. However, population-specific burden of CNVs on miRNA genes and the complexities created towards the phenotype is not known. From a total of 44109 CNVs investigated from 1715 individuals across 12 populations using high-throughput arrays, 4007 miRNA-CNVs (∼ 9%) consisting 6542 (∼ 5%) miRNA genes with a total of 333 (∼ 5%) singleton miRNA genes were identified. We found miRNA-CNVs across the genomes of individuals showing multiple hits in many targets, co-regulated under the same pathway. This study proposes four mechanisms unraveling the many complexities in miRNA genes, targets and co-regulated miRNA genes towards establishment of phenotypic diversity.", "link"=>"http://www.mendeley.com/research/copy-number-variations-burden-mirna-genes-reveals-layers-complexities-involved-regulation-pathways-p", "reader_count"=>18, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Librarian"=>1, "Researcher"=>2, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>5, "Student > Master"=>3, "Other"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Librarian"=>1, "Researcher"=>2, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>5, "Student > Master"=>3, "Other"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>12, "Medicine and Dentistry"=>1, "Social Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>12}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>2}}, "group_count"=>0}

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  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1403894/Figure_3.tif"], "description"=>"<p>a) Distribution of copy number states of the miRNA CNVs across 12 populations; b) represents the mean CN state across populations and c) represents the male-female distribution of miRNA genes under CNVs.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "Heredity", "Human genetics", "Molecular genetics", "genomics", "Chromosome biology", "Comparative genomics", "Functional genomics", "Genome complexity", "Genome evolution", "Structural genomics", "mirna"], "article_id"=>948943, "categories"=>["Biological Sciences"], "users"=>["Avinash M. Veerappa", "Megha Murthy N", "Sangeetha Vishweswaraiah", "Kusuma Lingaiah", "Raviraj V. Suresh", "Somanna Ajjamada Nachappa", "Nelchi Prashali", "Sangeetha Nuggehalli Yadav", "Manjula Arsikere Srikanta", "Dinesh S. Manjegowda", "Keshava B. Seshachalam", "Nallur B. Ramachandra"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0090391.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Copy_Number_State_and_Sex_bias_in_miRNA_sub_genome_/948943", "title"=>"Copy Number State and Sex bias in miRNA sub-genome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-28 03:57:47"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1403902/Figure_4.tif"], "description"=>"<p>CNV miRNA pathway showing the CNV burden of miRNA genes and its interaction with target proteins indicating the involvement in biological functions and diseases.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "Heredity", "Human genetics", "Molecular genetics", "genomics", "Chromosome biology", "Comparative genomics", "Functional genomics", "Genome complexity", "Genome evolution", "Structural genomics", "mirna", "pathway", "cnv", "genes", "proteins", "functions"], "article_id"=>948950, "categories"=>["Biological Sciences"], "users"=>["Avinash M. Veerappa", "Megha Murthy N", "Sangeetha Vishweswaraiah", "Kusuma Lingaiah", "Raviraj V. Suresh", "Somanna Ajjamada Nachappa", "Nelchi Prashali", "Sangeetha Nuggehalli Yadav", "Manjula Arsikere Srikanta", "Dinesh S. Manjegowda", "Keshava B. Seshachalam", "Nallur B. Ramachandra"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0090391.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_CNV_miRNA_pathway_showing_the_CNV_burden_of_miRNA_genes_and_its_interaction_with_target_proteins_indicating_the_involvement_in_biological_functions_and_diseases_/948950", "title"=>"CNV miRNA pathway showing the CNV burden of miRNA genes and its interaction with target proteins indicating the involvement in biological functions and diseases.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-28 03:57:47"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1403907/Figure_5.tif"], "description"=>"<p>Representation of the different levels of complexities (a–h) present in the genome as a result of CNV influence on the miRNA genes, their targets and protein interactors. The ‘+’ and ‘−’ sign beside each gene indicates the CNV type of duplication and deletion, “I” and “P” indicates the overlapping status of CNVs and the numerical indicate the CN state.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "Heredity", "Human genetics", "Molecular genetics", "genomics", "Chromosome biology", "Comparative genomics", "Functional genomics", "Genome complexity", "Genome evolution", "Structural genomics", "mirna", "cnv"], "article_id"=>948955, "categories"=>["Biological Sciences"], "users"=>["Avinash M. Veerappa", "Megha Murthy N", "Sangeetha Vishweswaraiah", "Kusuma Lingaiah", "Raviraj V. Suresh", "Somanna Ajjamada Nachappa", "Nelchi Prashali", "Sangeetha Nuggehalli Yadav", "Manjula Arsikere Srikanta", "Dinesh S. Manjegowda", "Keshava B. Seshachalam", "Nallur B. Ramachandra"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0090391.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Complexities_of_miRNA_CNV_effect_on_genes_/948955", "title"=>"Complexities of miRNA CNV effect on genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-28 03:57:47"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1403908/Table_1.xls"], "description"=>"<p>Distribution of miRNA CNVs and genes across 12 populations.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "Heredity", "Human genetics", "Molecular genetics", "genomics", "Chromosome biology", "Comparative genomics", "Functional genomics", "Genome complexity", "Genome evolution", "Structural genomics", "mirna", "cnvs", "genes", "12"], "article_id"=>948956, "categories"=>["Biological Sciences"], "users"=>["Avinash M. Veerappa", "Megha Murthy N", "Sangeetha Vishweswaraiah", "Kusuma Lingaiah", "Raviraj V. Suresh", "Somanna Ajjamada Nachappa", "Nelchi Prashali", "Sangeetha Nuggehalli Yadav", "Manjula Arsikere Srikanta", "Dinesh S. Manjegowda", "Keshava B. Seshachalam", "Nallur B. Ramachandra"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0090391.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Distribution_of_miRNA_CNVs_and_genes_across_12_populations_/948956", "title"=>"Distribution of miRNA CNVs and genes across 12 populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-28 03:57:47"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1403910/Table_2.xls"], "description"=>"<p>Population-wise and global frequency of recurrent miRNA-CNVs shared across 12 populations.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "Heredity", "Human genetics", "Molecular genetics", "genomics", "Chromosome biology", "Comparative genomics", "Functional genomics", "Genome complexity", "Genome evolution", "Structural genomics", "recurrent", "mirna-cnvs", "12"], "article_id"=>948958, "categories"=>["Biological Sciences"], "users"=>["Avinash M. Veerappa", "Megha Murthy N", "Sangeetha Vishweswaraiah", "Kusuma Lingaiah", "Raviraj V. Suresh", "Somanna Ajjamada Nachappa", "Nelchi Prashali", "Sangeetha Nuggehalli Yadav", "Manjula Arsikere Srikanta", "Dinesh S. Manjegowda", "Keshava B. Seshachalam", "Nallur B. Ramachandra"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0090391.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Population_wise_and_global_frequency_of_recurrent_miRNA_CNVs_shared_across_12_populations_/948958", "title"=>"Population-wise and global frequency of recurrent miRNA-CNVs shared across 12 populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-28 03:57:47"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1403911/Table_3.xls"], "description"=>"<p>Functional and disease association annotation of the miRNA genes under the CNV burden.</p>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "Heredity", "Human genetics", "Molecular genetics", "genomics", "Chromosome biology", "Comparative genomics", "Functional genomics", "Genome complexity", "Genome evolution", "Structural genomics", "annotation", "mirna", "genes", "cnv"], "article_id"=>948959, "categories"=>["Biological Sciences"], "users"=>["Avinash M. Veerappa", "Megha Murthy N", "Sangeetha Vishweswaraiah", "Kusuma Lingaiah", "Raviraj V. Suresh", "Somanna Ajjamada Nachappa", "Nelchi Prashali", "Sangeetha Nuggehalli Yadav", "Manjula Arsikere Srikanta", "Dinesh S. Manjegowda", "Keshava B. Seshachalam", "Nallur B. Ramachandra"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0090391.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Functional_and_disease_association_annotation_of_the_miRNA_genes_under_the_CNV_burden_/948959", "title"=>"Functional and disease association annotation of the miRNA genes under the CNV burden.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-28 03:57:47"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1403925/Figure_S1.tif", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1403926/Figure_S2.tif", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1403927/Figure_S3.tif", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/1403928/Figure_S4.tif"], "description"=>"<div><p>MicroRNAs are involved in post-transcriptional down-regulation of gene expression. Variations in miRNA genes can severely affect downstream-regulated genes and their pathways. However, population-specific burden of CNVs on miRNA genes and the complexities created towards the phenotype is not known. From a total of 44109 CNVs investigated from 1715 individuals across 12 populations using high-throughput arrays, 4007 miRNA-CNVs (∼9%) consisting 6542 (∼5%) miRNA genes with a total of 333 (∼5%) singleton miRNA genes were identified. We found miRNA-CNVs across the genomes of individuals showing multiple hits in many targets, co-regulated under the same pathway. This study proposes four mechanisms unraveling the many complexities in miRNA genes, targets and co-regulated miRNA genes towards establishment of phenotypic diversity.</p></div>", "links"=>[], "tags"=>["genetics", "Genetic mutation", "Heredity", "Human genetics", "Molecular genetics", "genomics", "Chromosome biology", "Comparative genomics", "Functional genomics", "Genome complexity", "Genome evolution", "Structural genomics", "variations", "mirna", "genes", "reveals", "layers", "complexities", "pathways", "phenotypic"], "article_id"=>948973, "categories"=>["Biological Sciences"], "users"=>["Avinash M. Veerappa", "Megha Murthy N", "Sangeetha Vishweswaraiah", "Kusuma Lingaiah", "Raviraj V. Suresh", "Somanna Ajjamada Nachappa", "Nelchi Prashali", "Sangeetha Nuggehalli Yadav", "Manjula Arsikere Srikanta", "Dinesh S. Manjegowda", "Keshava B. Seshachalam", "Nallur B. Ramachandra"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0090391"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Copy_Number_Variations_Burden_on_miRNA_Genes_Reveals_Layers_of_Complexities_Involved_in_the_Regulation_of_Pathways_and_Phenotypic_Expression_/948973", "title"=>"Copy Number Variations Burden on miRNA Genes Reveals Layers of Complexities Involved in the Regulation of Pathways and Phenotypic Expression", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-02-28 03:57:47"}

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Relative Metric

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