The Reality of Pervasive Transcription
Publication Date
July 12, 2011
Journal
PLOS Biology
Authors
Michael B. Clark, Paulo P. Amaral, Felix J. Schlesinger, Marcel E. Dinger, et al
Volume
9
Issue
7
Pages
e1000625
DOI
https://dx.plos.org/10.1371/journal.pbio.1000625
Publisher URL
http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.1000625
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/21765801
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3134446
Europe PMC
http://europepmc.org/abstract/MED/21765801
Web of Science
000293219800001
Scopus
79960911703
Mendeley
http://www.mendeley.com/research/reality-pervasive-transcription
Events
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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/757277"], "description"=>"<p>The Clark et al. transfrags are based on data generated as part of the ENCODE transcriptome project from K562 cell polyA+ RNA. The transfrags are generated from 5-bp two-color tiling arrays (MinRun  = 40 bp, MaxGap  = 40 bp). The seqfrags are based on 200 million paired-end 76 bp reads generated on the Illumina sequencing platform. Any detected region that overlaps an annotated exon is scored positive, all others negative. Fewer exons are detected overall (compared to van Bakel et al. <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000625#pbio.1000625-vanBakel1\" target=\"_blank\">[2]</a>), likely reflecting the difference between a relatively homogeneous cell line and complex tissue like brain.</p>", "links"=>[], "tags"=>["curves", "overlap", "transcribed", "regions", "experiments", "annotated", "exons", "gencode", "ucsc", "genes", "genome"], "article_id"=>427613, "categories"=>["Genetics"], "users"=>["Michael B. Clark", "Paulo P. Amaral", "Felix J. Schlesinger", "Marcel E. Dinger", "Ryan J. Taft", "John L. Rinn", "Chris P. Ponting", "Peter F. Stadler", "Kevin V. Morris", "Antonin Morillon", "Joel S. Rozowsky", "Mark B. Gerstein", "Claes Wahlestedt", "Yoshihide Hayashizaki", "Piero Carninci", "Thomas R. Gingeras", "John S. Mattick"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1000625.g001", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Precision_recall_curves_for_the_overlap_of_transcribed_regions_transfrags_detected_in_different_experiments_and_annotated_exons_from_GENCODE_version_4_and_the_UCSC_known_genes_track_from_the_UCSC_Genome_Browser_/427613", "title"=>"Precision recall curves for the overlap of transcribed regions (transfrags) detected in different experiments and annotated exons (from GENCODE version 4 and the UCSC known genes track from the UCSC Genome Browser).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-12 02:06:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/381224", "https://ndownloader.figshare.com/files/381256", "https://ndownloader.figshare.com/files/381283", "https://ndownloader.figshare.com/files/381312", "https://ndownloader.figshare.com/files/381341", "https://ndownloader.figshare.com/files/381368", "https://ndownloader.figshare.com/files/381390", "https://ndownloader.figshare.com/files/381406"], "description"=>"The Reality of Pervasive Transcription", "links"=>[], "tags"=>["pervasive", "transcription"], "article_id"=>135302, "categories"=>["Genetics"], "users"=>["Michael B. Clark", "Paulo P. Amaral", "Felix J. Schlesinger", "Marcel E. Dinger", "Ryan J. Taft", "John L. Rinn", "Chris P. Ponting", "Peter F. Stadler", "Kevin V. Morris", "Antonin Morillon", "Joel S. Rozowsky", "Mark B. Gerstein", "Claes Wahlestedt", "Yoshihide Hayashizaki", "Piero Carninci", "Thomas R. Gingeras", "John S. Mattick"], "doi"=>["https://dx.doi.org/10.1371/journal.pbio.1000625.s001", "https://dx.doi.org/10.1371/journal.pbio.1000625.s002", "https://dx.doi.org/10.1371/journal.pbio.1000625.s003", "https://dx.doi.org/10.1371/journal.pbio.1000625.s004", "https://dx.doi.org/10.1371/journal.pbio.1000625.s005", "https://dx.doi.org/10.1371/journal.pbio.1000625.s006", "https://dx.doi.org/10.1371/journal.pbio.1000625.s007", "https://dx.doi.org/10.1371/journal.pbio.1000625.s008"], "stats"=>{"downloads"=>6, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Reality_of_Pervasive_Transcription/135302", "title"=>"The Reality of Pervasive Transcription", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-07-12 01:28:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/757383"], "description"=>"<p>The figure shows the abundance of sequence reads mapped to the <i>HAR1A</i> locus <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000625#pbio.1000625-Pollard1\" target=\"_blank\">[43]</a> (green) and the TU created from these tags by van Bakel et al. using TopHat (red) <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000625#pbio.1000625-Trapnell2\" target=\"_blank\">[44]</a>. In contrast, the Clark et al. TU created by reanalysis of sequence reads using Cufflinks <a href=\"http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000625#pbio.1000625-Trapnell1\" target=\"_blank\">[28]</a> includes the extended 5′ and 3′ exonic sequences (dark blue).</p>", "links"=>[], "tags"=>["intron", "transcriptional", "units", "bakel", "et"], "article_id"=>427730, "categories"=>["Genetics"], "users"=>["Michael B. Clark", "Paulo P. Amaral", "Felix J. Schlesinger", "Marcel E. Dinger", "Ryan J. Taft", "John L. Rinn", "Chris P. Ponting", "Peter F. Stadler", "Kevin V. Morris", "Antonin Morillon", "Joel S. Rozowsky", "Mark B. Gerstein", "Claes Wahlestedt", "Yoshihide Hayashizaki", "Piero Carninci", "Thomas R. Gingeras", "John S. Mattick"], "doi"=>"https://dx.doi.org/10.1371/journal.pbio.1000625.g002", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Poor_coverage_of_single_intron_transcriptional_units_TUs_by_van_Bakel_et_al_2_/427730", "title"=>"Poor coverage of single intron transcriptional units (TUs) by van Bakel et al. [<b>2</b>].", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-07-12 02:08:50"}

PMC Usage Stats | Further Information

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Relative Metric

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