Entropy-Based Model for MiRNA Isoform Analysis
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{"title"=>"Entropy-based model for MiRNA isoform analysis", "type"=>"journal", "authors"=>[{"first_name"=>"Shengqin", "last_name"=>"Wang", "scopus_author_id"=>"54080744000"}, {"first_name"=>"Jing", "last_name"=>"Tu", "scopus_author_id"=>"36169668600"}, {"first_name"=>"Lei", "last_name"=>"Wang", "scopus_author_id"=>"57070615400"}, {"first_name"=>"Zuhong", "last_name"=>"Lu", "scopus_author_id"=>"55637289700"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84925428044", "pmid"=>"25785816", "scopus"=>"2-s2.0-84925428044", "pui"=>"603271460", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0118856"}, "id"=>"a4f80eac-6567-313e-a6ae-2ce36b8243ff", "abstract"=>"MiRNAs have been widely studied due to their important post-transcriptional regulatory roles in gene expression. Many reports have demonstrated the evidence of miRNA isoform products (isomiRs) in high-throughput small RNA sequencing data. However, the biological function involved in these molecules is still not well investigated. Here, we developed a Shannon entropy-based model to estimate isomiR expression profiles of high-throughput small RNA sequencing data extracted from miRBase webserver. By using the Kolmogorov-Smirnov statistical test (KS test), we demonstrated that the 5p and 3p miRNAs present more variants than the single arm miRNAs. We also found that the isomiR variant, except the 3' isomiR variant, is strongly correlated with Minimum Free Energy (MFE) of pre-miRNA, suggesting the intrinsic feature of pre-miRNA should be one of the important factors for the miRNA regulation. The functional enrichment analysis showed that the miRNAs with high variation, particularly the 5' end variation, are enriched in a set of critical functions, supporting these molecules should not be randomly produced. Our results provide a probabilistic framework for miRNA isoforms analysis, and give functional insights into pre-miRNA processing.", "link"=>"http://www.mendeley.com/research/entropybased-model-mirna-isoform-analysis", "reader_count"=>20, "reader_count_by_academic_status"=>{"Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>1, "Unspecified"=>2}, "reader_count_by_user_role"=>{"Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>3, "Student > Bachelor"=>3, "Lecturer"=>1, "Professor"=>1, "Unspecified"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>8, "Psychology"=>1, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"New Zealand"=>1, "Colombia"=>1, "United States"=>2, "Denmark"=>1, "Germany"=>1}, "group_count"=>0}

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1957335"], "description"=>"<p>Sequences located in the dotted frame (canonical mature miRNA region ± 4 nt) are accepted for <i>MIH</i> calculation. Bases located in the left rectangle are used for <i>MIH</i>5 calculation, and those located in the right rectangle are used for <i>MIH</i>3 calculation (including the gap character “-”).</p>", "links"=>[], "tags"=>["estimate isomiR expression profiles", "isomiR variant", "miRNA isoforms analysis", "mfe", "RNA sequencing data", "gene expression", "miRNA isoform products", "miRNA regulation", "5 p", "Minimum Free Energy", "arm miRNAs", "Many reports", "miRBase webserver", "enrichment analysis", "3 p miRNAs", "ks", "MiRNA Isoform Analysis MiRNAs"], "article_id"=>1340693, "categories"=>["Biological Sciences"], "users"=>["Shengqin Wang", "Jing Tu", "Lei Wang", "Zuhong Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0118856.g001", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Region_selection_for_MIH_calculation_/1340693", "title"=>"Region selection for <i>MIH</i> calculation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-18 03:21:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1957339"], "description"=>"<p>Significantly enriched functions of the MiRNAs with the top 15% <i>MIH5</i> values.</p>", "links"=>[], "tags"=>["estimate isomiR expression profiles", "isomiR variant", "miRNA isoforms analysis", "mfe", "RNA sequencing data", "gene expression", "miRNA isoform products", "miRNA regulation", "5 p", "Minimum Free Energy", "arm miRNAs", "Many reports", "miRBase webserver", "enrichment analysis", "3 p miRNAs", "ks", "MiRNA Isoform Analysis MiRNAs"], "article_id"=>1340697, "categories"=>["Biological Sciences"], "users"=>["Shengqin Wang", "Jing Tu", "Lei Wang", "Zuhong Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0118856.t001", "stats"=>{"downloads"=>6, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significantly_enriched_functions_of_the_MiRNAs_with_the_top_15_MIH5_values_/1340697", "title"=>"Significantly enriched functions of the MiRNAs with the top 15% <i>MIH5</i> values.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-18 03:21:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1957337"], "description"=>"<p>(A) <i>MIH</i> and length of pre-miRNA; (B) <i>MIH</i> and MFE; (C) <i>MIH5</i> and length of pre-miRNA; (D) <i>MIH5</i> and MFE; (E) <i>MIH3</i> and length of pre-miRNA; (F) <i>MIH3</i> and MFE; (G) <i>MIH</i> and count of reads; (H) High <i>MIH</i> and low <i>MIH</i>. High and low <i>MIH</i> values are calculated by comparing the <i>MIH</i> values between the 5p and 3p miRNAs from the same precursor.</p>", "links"=>[], "tags"=>["estimate isomiR expression profiles", "isomiR variant", "miRNA isoforms analysis", "mfe", "RNA sequencing data", "gene expression", "miRNA isoform products", "miRNA regulation", "5 p", "Minimum Free Energy", "arm miRNAs", "Many reports", "miRBase webserver", "enrichment analysis", "3 p miRNAs", "ks", "MiRNA Isoform Analysis MiRNAs"], "article_id"=>1340695, "categories"=>["Biological Sciences"], "users"=>["Shengqin Wang", "Jing Tu", "Lei Wang", "Zuhong Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0118856.g003", "stats"=>{"downloads"=>0, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pearson_8217_s_correlation_analysis_/1340695", "title"=>"Pearson’s correlation analysis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-18 03:21:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1957338"], "description"=>"<p>The X-axis displays the proportion of the top isoform entropy miRNAs. The Y-axis is the number of significantly enriched function terms.</p>", "links"=>[], "tags"=>["estimate isomiR expression profiles", "isomiR variant", "miRNA isoforms analysis", "mfe", "RNA sequencing data", "gene expression", "miRNA isoform products", "miRNA regulation", "5 p", "Minimum Free Energy", "arm miRNAs", "Many reports", "miRBase webserver", "enrichment analysis", "3 p miRNAs", "ks", "MiRNA Isoform Analysis MiRNAs"], "article_id"=>1340696, "categories"=>["Biological Sciences"], "users"=>["Shengqin Wang", "Jing Tu", "Lei Wang", "Zuhong Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0118856.g004", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_The_functional_enrichment_analysis_for_miRNA_with_high_isoform_entropy_values_by_TAM_tool_/1340696", "title"=>"(A) The functional enrichment analysis for miRNA with high isoform entropy values by TAM tool.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-18 03:21:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/1957336"], "description"=>"<p>(A) <i>MIH</i> distribution of all mature miRNAs after filter. (B) KS-test comparison cumulative fraction plot. Solid line indicates the cumulative distribution of mature miRNA <i>MIH</i> values from both 5’ and 3’ arms of the hairpin precursors (the 3p and 5p miRNAs). Dot line shows the cumulative distribution of mature miRNA <i>MIH</i> values from only single arms (the single arm miRNAs).</p>", "links"=>[], "tags"=>["estimate isomiR expression profiles", "isomiR variant", "miRNA isoforms analysis", "mfe", "RNA sequencing data", "gene expression", "miRNA isoform products", "miRNA regulation", "5 p", "Minimum Free Energy", "arm miRNAs", "Many reports", "miRBase webserver", "enrichment analysis", "3 p miRNAs", "ks", "MiRNA Isoform Analysis MiRNAs"], "article_id"=>1340694, "categories"=>["Biological Sciences"], "users"=>["Shengqin Wang", "Jing Tu", "Lei Wang", "Zuhong Lu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0118856.g002", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_MIH_values_/1340694", "title"=>"Distribution of <i>MIH</i> values.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-18 03:21:10"}

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  • {"unique-ip"=>"15", "full-text"=>"14", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2015", "month"=>"11"}
  • {"unique-ip"=>"17", "full-text"=>"9", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2015", "month"=>"12"}
  • {"unique-ip"=>"23", "full-text"=>"20", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2016", "month"=>"1"}
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  • {"unique-ip"=>"9", "full-text"=>"8", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"5"}
  • {"unique-ip"=>"15", "full-text"=>"13", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"6"}
  • {"unique-ip"=>"9", "full-text"=>"8", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2016", "month"=>"7"}
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  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
  • {"unique-ip"=>"8", "full-text"=>"6", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"11"}
  • {"unique-ip"=>"1", "full-text"=>"0", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"2"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"3"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"4"}
  • {"unique-ip"=>"16", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"4", "cited-by"=>"1", "year"=>"2017", "month"=>"5"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"6"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"15", "full-text"=>"6", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"4", "cited-by"=>"1", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"17", "full-text"=>"16", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
  • {"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
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  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"6", "full-text"=>"2", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"7", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"13", "full-text"=>"13", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"5", "full-text"=>"2", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"11", "full-text"=>"6", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}

Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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Net::HTTPInternalServerError

Source
Counter
Time
2019-04-06 02:38:25 UTC
Target URL
http://counter-101.soma.plos.org/api/v1.0/stats/doi/10.1371%2Fjournal.pone.0118856
Trace

/app/models/concerns/networkable.rb:21:in `get_result'
/app/models/source.rb:165:in `get_data'
/app/models/retrieval_status.rb:47:in `perform_get_data'
/app/jobs/source_job.rb:52:in `block (2 levels) in perform'
/app/jobs/source_job.rb:51:in `block in perform'
/app/jobs/source_job.rb:35:in `each'
/app/jobs/source_job.rb:35:in `perform'