miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets
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{"title"=>"MiRSystem: An integrated system for characterizing enriched functions and pathways of microRNA targets", "type"=>"journal", "authors"=>[{"first_name"=>"Tzu Pin", "last_name"=>"Lu", "scopus_author_id"=>"35332513800"}, {"first_name"=>"Chien Yueh", "last_name"=>"Lee", "scopus_author_id"=>"50661483900"}, {"first_name"=>"Mong Hsun", "last_name"=>"Tsai", "scopus_author_id"=>"7403551410"}, {"first_name"=>"Yu Chiao", "last_name"=>"Chiu", "scopus_author_id"=>"55330817500"}, {"first_name"=>"Chuhsing Kate", "last_name"=>"Hsiao", "scopus_author_id"=>"34667832900"}, {"first_name"=>"Liang Chuan", "last_name"=>"Lai", "scopus_author_id"=>"7202616267"}, {"first_name"=>"Eric Y.", "last_name"=>"Chuang", "scopus_author_id"=>"7005960101"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"365367016", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"22870325", "sgr"=>"84864777932", "scopus"=>"2-s2.0-84864777932", "doi"=>"10.1371/journal.pone.0042390"}, "id"=>"e5522374-854a-359a-81f4-475e99797a2b", "abstract"=>"BACKGROUND Many prediction tools for microRNA (miRNA) targets have been developed, but inconsistent predictions were observed across multiple algorithms, which can make further analysis difficult. Moreover, the nomenclature of human miRNAs changes rapidly. To address these issues, we developed a web-based system, miRSystem, for converting queried miRNAs to the latest annotation and predicting the function of miRNA by integrating miRNA target gene prediction and function/pathway analyses. RESULTS First, queried miRNA IDs were converted to the latest annotated version to prevent potential conflicts resulting from multiple aliases. Next, by combining seven algorithms and two validated databases, potential gene targets of miRNAs and their functions were predicted based on the consistency across independent algorithms and observed/expected ratios. Lastly, five pathway databases were included to characterize the enriched pathways of target genes through bootstrap approaches. Based on the enriched pathways of target genes, the functions of queried miRNAs could be predicted. CONCLUSIONS MiRSystem is a user-friendly tool for predicting the target genes and their associated pathways for many miRNAs simultaneously. The web server and the documentation are freely available at http://mirsystem.cgm.ntu.edu.tw/.", "link"=>"http://www.mendeley.com/research/mirsystem-integrated-system-characterizing-enriched-functions-pathways-microrna-targets", "reader_count"=>89, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>5, "Librarian"=>1, "Student > Doctoral Student"=>6, "Researcher"=>24, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>4, "Student > Master"=>12, "Other"=>1, "Student > Bachelor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>5, "Librarian"=>1, "Student > Doctoral Student"=>6, "Researcher"=>24, "Student > Ph. D. Student"=>29, "Student > Postgraduate"=>4, "Student > Master"=>12, "Other"=>1, "Student > Bachelor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Biochemistry, Genetics and Molecular Biology"=>14, "Mathematics"=>1, "Agricultural and Biological Sciences"=>49, "Medicine and Dentistry"=>8, "Arts and Humanities"=>1, "Social Sciences"=>1, "Computer Science"=>9, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>8}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>49}, "Computer Science"=>{"Computer Science"=>9}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>14}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>5}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "Netherlands"=>1, "Hungary"=>1, "United States"=>1, "Luxembourg"=>2, "Brazil"=>1, "United Kingdom"=>2, "Portugal"=>1, "Germany"=>1, "India"=>1}, "group_count"=>6}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/312725", "https://ndownloader.figshare.com/files/312799", "https://ndownloader.figshare.com/files/312888", "https://ndownloader.figshare.com/files/312980", "https://ndownloader.figshare.com/files/313054", "https://ndownloader.figshare.com/files/313106", "https://ndownloader.figshare.com/files/313158", "https://ndownloader.figshare.com/files/313222"], "description"=>"<div><h3>Background</h3><p>Many prediction tools for microRNA (miRNA) targets have been developed, but inconsistent predictions were observed across multiple algorithms, which can make further analysis difficult. Moreover, the nomenclature of human miRNAs changes rapidly. To address these issues, we developed a web-based system, miRSystem, for converting queried miRNAs to the latest annotation and predicting the function of miRNA by integrating miRNA target gene prediction and function/pathway analyses.</p> <h3>Results</h3><p>First, queried miRNA IDs were converted to the latest annotated version to prevent potential conflicts resulting from multiple aliases. Next, by combining seven algorithms and two validated databases, potential gene targets of miRNAs and their functions were predicted based on the consistency across independent algorithms and observed/expected ratios. Lastly, five pathway databases were included to characterize the enriched pathways of target genes through bootstrap approaches. Based on the enriched pathways of target genes, the functions of queried miRNAs could be predicted.</p> <h3>Conclusions</h3><p>MiRSystem is a user-friendly tool for predicting the target genes and their associated pathways for many miRNAs simultaneously. The web server and the documentation are freely available at <a href=\"http://mirsystem.cgm.ntu.edu.tw/\">http://mirsystem.cgm.ntu.edu.tw/</a>.</p> </div>", "links"=>[], "tags"=>["characterizing", "enriched", "functions", "pathways", "microrna", "targets"], "article_id"=>121689, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Tzu-Pin Lu", "Chien-Yueh Lee", "Mong-Hsun Tsai", "Yu-Chiao Chiu", "Chuhsing Kate Hsiao", "Liang-Chuan Lai", "Eric Y. Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0042390.s001", "https://dx.doi.org/10.1371/journal.pone.0042390.s002", "https://dx.doi.org/10.1371/journal.pone.0042390.s003", "https://dx.doi.org/10.1371/journal.pone.0042390.s004", "https://dx.doi.org/10.1371/journal.pone.0042390.s005", "https://dx.doi.org/10.1371/journal.pone.0042390.s006", "https://dx.doi.org/10.1371/journal.pone.0042390.s007", "https://dx.doi.org/10.1371/journal.pone.0042390.s008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/miRSystem_An_Integrated_System_for_Characterizing_Enriched_Functions_and_Pathways_of_MicroRNA_Targets/121689", "title"=>"miRSystem: An Integrated System for Characterizing Enriched Functions and Pathways of MicroRNA Targets", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-08-01 00:28:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/598265"], "description"=>"<p>The green boxes indicate the data input and output. The purple rectangle with a dotted outline represents the miRSystem core. The three major components of miRSystem (blue boxes) are the miRNA ID converter, statistical analysis tools, and web application server. The target prediction algorithms (upper yellow cylinder) constitute 7 programs (white boxes) and 2 experimentally validated data sets (red boxes). The pathway prediction module (lower yellow cylinder) includes the information from 5 databases (orange boxes).</p>", "links"=>[], "tags"=>["overview"], "article_id"=>268756, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Tzu-Pin Lu", "Chien-Yueh Lee", "Mong-Hsun Tsai", "Yu-Chiao Chiu", "Chuhsing Kate Hsiao", "Liang-Chuan Lai", "Eric Y. Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0042390.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_overview_of_miRSystem_/268756", "title"=>"An overview of miRSystem.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-01 02:25:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/598398"], "description"=>"<p>A hierarchical menu is shown in the left panel and the queried and analyzed results are shown in the main window.</p>", "links"=>[], "tags"=>["interface"], "article_id"=>268888, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Tzu-Pin Lu", "Chien-Yueh Lee", "Mong-Hsun Tsai", "Yu-Chiao Chiu", "Chuhsing Kate Hsiao", "Liang-Chuan Lai", "Eric Y. Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0042390.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Graphical_user_interface_in_miRSystem_/268888", "title"=>"Graphical user interface in miRSystem.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-01 02:28:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/598529"], "description"=>"<p>miRConverter allows two types of query format: (A) miRNA sequence and (B) accession number.</p>", "links"=>[], "tags"=>["genetics and genomics", "Computational biology", "computer science"], "article_id"=>269016, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Tzu-Pin Lu", "Chien-Yueh Lee", "Mong-Hsun Tsai", "Yu-Chiao Chiu", "Chuhsing Kate Hsiao", "Liang-Chuan Lai", "Eric Y. Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0042390.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Screenshots_of_miRConverter_/269016", "title"=>"Screenshots of miRConverter.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-01 02:30:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/598630"], "description"=>"<p>(A) The miRNA input interface. (B) Tabulated results of enriched pathways of miRNA target genes based on the consistency across multiple algorithms and observed/expected ratios.</p>", "links"=>[], "tags"=>["mirna", "genes"], "article_id"=>269123, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Tzu-Pin Lu", "Chien-Yueh Lee", "Mong-Hsun Tsai", "Yu-Chiao Chiu", "Chuhsing Kate Hsiao", "Liang-Chuan Lai", "Eric Y. Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0042390.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_miRNA_target_genes_in_miRSystem_/269123", "title"=>"Identification of miRNA target genes in miRSystem.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-01 02:32:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/598814"], "description"=>"<p>(A) The graphical output of enriched pathways of miRNA target genes. Y-axis: −log (<i>P</i>-value). (B) Tabulated results of enriched pathways of miRNA target genes using a pathway-ranking algorithm that incorporates weighting based on the expression levels of a given miRNA set.</p>", "links"=>[], "tags"=>["pathway", "enrichment"], "article_id"=>269308, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Tzu-Pin Lu", "Chien-Yueh Lee", "Mong-Hsun Tsai", "Yu-Chiao Chiu", "Chuhsing Kate Hsiao", "Liang-Chuan Lai", "Eric Y. Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0042390.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_pathway_enrichment_analysis_/269308", "title"=>"Results of pathway enrichment analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-01 02:35:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/598947"], "description"=>"<p>The genes highlighted in red color are predicted to be regulated by queried miRNAs.</p>", "links"=>[], "tags"=>["embedded", "hyperlink", "kegg"], "article_id"=>269436, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Tzu-Pin Lu", "Chien-Yueh Lee", "Mong-Hsun Tsai", "Yu-Chiao Chiu", "Chuhsing Kate Hsiao", "Liang-Chuan Lai", "Eric Y. Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0042390.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_embedded_hyperlink_to_KEGG_database_/269436", "title"=>"Illustration of embedded hyperlink to KEGG database.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-01 02:37:16"}
  • {"files"=>["https://ndownloader.figshare.com/files/599063"], "description"=>"<p>(A) Gene input interface for query of regulatory miRNAs. (B) Tabulated results of prediction of regulatory miRNAs.</p>", "links"=>[], "tags"=>["mirnas"], "article_id"=>269552, "categories"=>["Information And Computing Sciences", "Biological Sciences", "Genetics"], "users"=>["Tzu-Pin Lu", "Chien-Yueh Lee", "Mong-Hsun Tsai", "Yu-Chiao Chiu", "Chuhsing Kate Hsiao", "Liang-Chuan Lai", "Eric Y. Chuang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0042390.g007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Identification_of_regulatory_miRNAs_from_predicted_target_genes_/269552", "title"=>"Identification of regulatory miRNAs from predicted target genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-08-01 02:39:12"}
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PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[375, 629, 760, 889, 1000, 1110, 1203, 1298, 1399, 1492, 1603, 1699, 1774, 1855, 1918, 1998, 2062, 2152, 2227, 2312, 2378, 2461, 2528, 2600, 2664]}, {"subject_area"=>"/Medicine and health sciences", "average_usage"=>[312, 547, 668, 769, 861, 953, 1046, 1135, 1224, 1307, 1388, 1464, 1536, 1606, 1676, 1744, 1812, 1882, 1954, 2020, 2089, 2155, 2218, 2282, 2344]}, {"subject_area"=>"/Medicine and health sciences/Hematology", "average_usage"=>[300, 532, 651, 749, 842, 929, 1022, 1106, 1192, 1267, 1351, 1423, 1489, 1553, 1631, 1694, 1764, 1835, 1899, 1964, 2027, 2087, 2159, 2228, 2280]}]}
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