deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data
Publication Date
May 19, 2011
Journal
PLOS Computational Biology
Authors
Andrew Mc Pherson, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, et al
Volume
7
Issue
5
Pages
e1001138
DOI
http://doi.org/10.1371/journal.pcbi.1001138
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1001138
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/21625565
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098195
Europe PMC
http://europepmc.org/abstract/MED/21625565
Web of Science
000291015800012
Scopus
79957829805
Mendeley
http://www.mendeley.com/research/defuse-algorithm-gene-fusion-discovery-tumor-rnaseq-data
Events
Loading … Spinner

CiteULike | Further Information

Mendeley | Further Information

{"title"=>"Defuse: An algorithm for gene fusion discovery in tumor rna-seq data", "type"=>"journal", "authors"=>[{"first_name"=>"Andrew", "last_name"=>"McPherson", "scopus_author_id"=>"36614383000"}, {"first_name"=>"Fereydoun", "last_name"=>"Hormozdiari", "scopus_author_id"=>"17343845300"}, {"first_name"=>"Abdalnasser", "last_name"=>"Zayed", "scopus_author_id"=>"26658814500"}, {"first_name"=>"Ryan", "last_name"=>"Giuliany", "scopus_author_id"=>"26658410500"}, {"first_name"=>"Gavin", "last_name"=>"Ha", "scopus_author_id"=>"36015155300"}, {"first_name"=>"Mark G.F.", "last_name"=>"Sun", "scopus_author_id"=>"36129779000"}, {"first_name"=>"Malachi", "last_name"=>"Griffith", "scopus_author_id"=>"7102075315"}, {"first_name"=>"Alireza", "last_name"=>"Moussavi", "scopus_author_id"=>"54385750800"}, {"first_name"=>"Janine", "last_name"=>"Senz", "scopus_author_id"=>"6507529905"}, {"first_name"=>"Nataliya", "last_name"=>"Melnyk", "scopus_author_id"=>"6506844507"}, {"first_name"=>"Marina", "last_name"=>"Pacheco", "scopus_author_id"=>"35269335800"}, {"first_name"=>"Marco A.", "last_name"=>"Marra", "scopus_author_id"=>"55553154800"}, {"first_name"=>"Martin", "last_name"=>"Hirst", "scopus_author_id"=>"10341470700"}, {"first_name"=>"Torsten O.", "last_name"=>"Nielsen", "scopus_author_id"=>"7201759696"}, {"first_name"=>"S. Cenk", "last_name"=>"Sahinalp", "scopus_author_id"=>"6603800467"}, {"first_name"=>"David", "last_name"=>"Huntsman", "scopus_author_id"=>"7003437964"}, {"first_name"=>"Sohrab P.", "last_name"=>"Shah", "scopus_author_id"=>"7403888751"}], "year"=>2011, "source"=>"PLoS Computational Biology", "identifiers"=>{"pui"=>"361907830", "sgr"=>"79957829805", "issn"=>"1553734X", "pmid"=>"21625565", "scopus"=>"2-s2.0-79957829805", "doi"=>"10.1371/journal.pcbi.1001138", "isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)"}, "id"=>"601a0e55-0e90-3620-a1fc-9cffcf56112c", "abstract"=>"Gene fusions created by somatic genomic rearrangements are known to play an important role in the onset and development of some cancers, such as lymphomas and sarcomas. RNA-Seq (whole transcriptome shotgun sequencing) is proving to be a useful tool for the discovery of novel gene fusions in cancer transcriptomes. However, algorithmic methods for the discovery of gene fusions using RNA-Seq data remain underdeveloped. We have developed deFuse, a novel computational method for fusion discovery in tumor RNA-Seq data. Unlike existing methods that use only unique best-hit alignments and consider only fusion boundaries at the ends of known exons, deFuse considers all alignments and all possible locations for fusion boundaries. As a result, deFuse is able to identify fusion sequences with demonstrably better sensitivity than previous approaches. To increase the specificity of our approach, we curated a list of 60 true positive and 61 true negative fusion sequences (as confirmed by RT-PCR), and have trained an adaboost classifier on 11 novel features of the sequence data. The resulting classifier has an estimated value of 0.91 for the area under the ROC curve. We have used deFuse to discover gene fusions in 40 ovarian tumor samples, one ovarian cancer cell line, and three sarcoma samples. We report herein the first gene fusions discovered in ovarian cancer. We conclude that gene fusions are not infrequent events in ovarian cancer and that these events have the potential to substantially alter the expression patterns of the genes involved; gene fusions should therefore be considered in efforts to comprehensively characterize the mutational profiles of ovarian cancer transcriptomes.", "link"=>"http://www.mendeley.com/research/defuse-algorithm-gene-fusion-discovery-tumor-rnaseq-data", "reader_count"=>389, "reader_count_by_academic_status"=>{"Unspecified"=>5, "Professor > Associate Professor"=>18, "Librarian"=>2, "Researcher"=>130, "Student > Doctoral Student"=>17, "Student > Ph. D. Student"=>109, "Student > Postgraduate"=>10, "Other"=>16, "Student > Master"=>48, "Student > Bachelor"=>16, "Lecturer"=>6, "Lecturer > Senior Lecturer"=>2, "Professor"=>10}, "reader_count_by_user_role"=>{"Unspecified"=>5, "Professor > Associate Professor"=>18, "Librarian"=>2, "Researcher"=>130, "Student > Doctoral Student"=>17, "Student > Ph. D. Student"=>109, "Student > Postgraduate"=>10, "Other"=>16, "Student > Master"=>48, "Student > Bachelor"=>16, "Lecturer"=>6, "Lecturer > Senior Lecturer"=>2, "Professor"=>10}, "reader_count_by_subject_area"=>{"Unspecified"=>11, "Agricultural and Biological Sciences"=>215, "Arts and Humanities"=>2, "Veterinary Science and Veterinary Medicine"=>2, "Computer Science"=>40, "Economics, Econometrics and Finance"=>2, "Engineering"=>7, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>64, "Mathematics"=>4, "Medicine and Dentistry"=>33, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>2, "Social Sciences"=>1, "Immunology and Microbiology"=>3, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>33}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Mathematics"=>{"Mathematics"=>4}, "Unspecified"=>{"Unspecified"=>11}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>2}, "Engineering"=>{"Engineering"=>7}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>215}, "Computer Science"=>{"Computer Science"=>40}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>64}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Republic of Singapore"=>1, "United States"=>12, "Japan"=>2, "Ukraine"=>1, "Egypt"=>1, "United Kingdom"=>5, "Switzerland"=>1, "New Zealand"=>1, "Canada"=>4, "Austria"=>1, "Sweden"=>1, "Netherlands"=>2, "Korea (South)"=>3, "Belgium"=>1, "Norway"=>2, "China"=>1, "Brazil"=>1, "Denmark"=>1, "Italy"=>3, "France"=>4, "Germany"=>1, "Indonesia"=>1}, "group_count"=>25}

CrossRef

Scopus | Further Information

{"@_fa"=>"true", "link"=>[{"@_fa"=>"true", "@ref"=>"self", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/79957829805"}, {"@_fa"=>"true", "@ref"=>"author-affiliation", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/79957829805?field=author,affiliation"}, {"@_fa"=>"true", "@ref"=>"scopus", "@href"=>"https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=79957829805&origin=inward"}, {"@_fa"=>"true", "@ref"=>"scopus-citedby", "@href"=>"https://www.scopus.com/inward/citedby.uri?partnerID=HzOxMe3b&scp=79957829805&origin=inward"}], "prism:url"=>"https://api.elsevier.com/content/abstract/scopus_id/79957829805", "dc:identifier"=>"SCOPUS_ID:79957829805", "eid"=>"2-s2.0-79957829805", "dc:title"=>"Defuse: An algorithm for gene fusion discovery in tumor rna-seq data", "dc:creator"=>"McPherson A.", "prism:publicationName"=>"PLoS Computational Biology", "prism:issn"=>"1553734X", "prism:eIssn"=>"15537358", "prism:volume"=>"7", "prism:issueIdentifier"=>"5", "prism:pageRange"=>nil, "prism:coverDate"=>"2011-05-01", "prism:coverDisplayDate"=>"May 2011", "prism:doi"=>"10.1371/journal.pcbi.1001138", "citedby-count"=>"266", "affiliation"=>[{"@_fa"=>"true", "affilname"=>"British Columbia Cancer Agency", "affiliation-city"=>"Vancouver", "affiliation-country"=>"Canada"}, {"@_fa"=>"true", "affilname"=>"Simon Fraser University", "affiliation-city"=>"Burnaby", "affiliation-country"=>"Canada"}], "pubmed-id"=>"21625565", "prism:aggregationType"=>"Journal", "subtype"=>"ar", "subtypeDescription"=>"Article", "article-number"=>"e1001138", "source-id"=>"4000151810", "openaccess"=>"1", "openaccessFlag"=>true}

Facebook

  • {"url"=>"http%3A%2F%2Fjournals.plos.org%2Fploscompbiol%2Farticle%3Fid%3D10.1371%252Fjournal.pcbi.1001138", "share_count"=>1, "like_count"=>0, "comment_count"=>0, "click_count"=>0, "total_count"=>1}

Journal Comments | Further Information

Twitter

Counter

  • {"month"=>"5", "year"=>"2011", "pdf_views"=>"223", "xml_views"=>"7", "html_views"=>"853"}
  • {"month"=>"6", "year"=>"2011", "pdf_views"=>"162", "xml_views"=>"13", "html_views"=>"591"}
  • {"month"=>"7", "year"=>"2011", "pdf_views"=>"81", "xml_views"=>"1", "html_views"=>"269"}
  • {"month"=>"8", "year"=>"2011", "pdf_views"=>"69", "xml_views"=>"1", "html_views"=>"230"}
  • {"month"=>"9", "year"=>"2011", "pdf_views"=>"95", "xml_views"=>"1", "html_views"=>"262"}
  • {"month"=>"10", "year"=>"2011", "pdf_views"=>"67", "xml_views"=>"2", "html_views"=>"266"}
  • {"month"=>"11", "year"=>"2011", "pdf_views"=>"72", "xml_views"=>"5", "html_views"=>"274"}
  • {"month"=>"12", "year"=>"2011", "pdf_views"=>"79", "xml_views"=>"0", "html_views"=>"265"}
  • {"month"=>"1", "year"=>"2012", "pdf_views"=>"67", "xml_views"=>"1", "html_views"=>"246"}
  • {"month"=>"2", "year"=>"2012", "pdf_views"=>"71", "xml_views"=>"3", "html_views"=>"323"}
  • {"month"=>"3", "year"=>"2012", "pdf_views"=>"73", "xml_views"=>"0", "html_views"=>"290"}
  • {"month"=>"4", "year"=>"2012", "pdf_views"=>"70", "xml_views"=>"2", "html_views"=>"293"}
  • {"month"=>"5", "year"=>"2012", "pdf_views"=>"89", "xml_views"=>"3", "html_views"=>"305"}
  • {"month"=>"6", "year"=>"2012", "pdf_views"=>"77", "xml_views"=>"5", "html_views"=>"316"}
  • {"month"=>"7", "year"=>"2012", "pdf_views"=>"85", "xml_views"=>"1", "html_views"=>"383"}
  • {"month"=>"8", "year"=>"2012", "pdf_views"=>"50", "xml_views"=>"12", "html_views"=>"212"}
  • {"month"=>"9", "year"=>"2012", "pdf_views"=>"55", "xml_views"=>"0", "html_views"=>"332"}
  • {"month"=>"10", "year"=>"2012", "pdf_views"=>"59", "xml_views"=>"0", "html_views"=>"349"}
  • {"month"=>"11", "year"=>"2012", "pdf_views"=>"72", "xml_views"=>"1", "html_views"=>"336"}
  • {"month"=>"12", "year"=>"2012", "pdf_views"=>"66", "xml_views"=>"4", "html_views"=>"409"}
  • {"month"=>"1", "year"=>"2013", "pdf_views"=>"61", "xml_views"=>"1", "html_views"=>"367"}
  • {"month"=>"2", "year"=>"2013", "pdf_views"=>"68", "xml_views"=>"2", "html_views"=>"675"}
  • {"month"=>"3", "year"=>"2013", "pdf_views"=>"71", "xml_views"=>"1", "html_views"=>"374"}
  • {"month"=>"4", "year"=>"2013", "pdf_views"=>"53", "xml_views"=>"0", "html_views"=>"391"}
  • {"month"=>"5", "year"=>"2013", "pdf_views"=>"69", "xml_views"=>"0", "html_views"=>"377"}
  • {"month"=>"6", "year"=>"2013", "pdf_views"=>"50", "xml_views"=>"0", "html_views"=>"375"}
  • {"month"=>"7", "year"=>"2013", "pdf_views"=>"50", "xml_views"=>"8", "html_views"=>"378"}
  • {"month"=>"8", "year"=>"2013", "pdf_views"=>"42", "xml_views"=>"3", "html_views"=>"315"}
  • {"month"=>"9", "year"=>"2013", "pdf_views"=>"53", "xml_views"=>"4", "html_views"=>"363"}
  • {"month"=>"10", "year"=>"2013", "pdf_views"=>"61", "xml_views"=>"1", "html_views"=>"373"}
  • {"month"=>"11", "year"=>"2013", "pdf_views"=>"60", "xml_views"=>"3", "html_views"=>"353"}
  • {"month"=>"12", "year"=>"2013", "pdf_views"=>"37", "xml_views"=>"1", "html_views"=>"300"}
  • {"month"=>"1", "year"=>"2014", "pdf_views"=>"61", "xml_views"=>"0", "html_views"=>"410"}
  • {"month"=>"2", "year"=>"2014", "pdf_views"=>"40", "xml_views"=>"1", "html_views"=>"345"}
  • {"month"=>"3", "year"=>"2014", "pdf_views"=>"60", "xml_views"=>"2", "html_views"=>"376"}
  • {"month"=>"4", "year"=>"2014", "pdf_views"=>"65", "xml_views"=>"1", "html_views"=>"382"}
  • {"month"=>"5", "year"=>"2014", "pdf_views"=>"62", "xml_views"=>"1", "html_views"=>"432"}
  • {"month"=>"6", "year"=>"2014", "pdf_views"=>"55", "xml_views"=>"2", "html_views"=>"388"}
  • {"month"=>"7", "year"=>"2014", "pdf_views"=>"80", "xml_views"=>"0", "html_views"=>"505"}
  • {"month"=>"8", "year"=>"2014", "pdf_views"=>"44", "xml_views"=>"2", "html_views"=>"325"}
  • {"month"=>"9", "year"=>"2014", "pdf_views"=>"60", "xml_views"=>"1", "html_views"=>"393"}
  • {"month"=>"10", "year"=>"2014", "pdf_views"=>"59", "xml_views"=>"8", "html_views"=>"458"}
  • {"month"=>"11", "year"=>"2014", "pdf_views"=>"47", "xml_views"=>"2", "html_views"=>"385"}
  • {"month"=>"12", "year"=>"2014", "pdf_views"=>"53", "xml_views"=>"3", "html_views"=>"292"}
  • {"month"=>"1", "year"=>"2015", "pdf_views"=>"36", "xml_views"=>"0", "html_views"=>"265"}
  • {"month"=>"2", "year"=>"2015", "pdf_views"=>"46", "xml_views"=>"0", "html_views"=>"283"}
  • {"month"=>"3", "year"=>"2015", "pdf_views"=>"39", "xml_views"=>"0", "html_views"=>"228"}
  • {"month"=>"4", "year"=>"2015", "pdf_views"=>"53", "xml_views"=>"1", "html_views"=>"242"}
  • {"month"=>"5", "year"=>"2015", "pdf_views"=>"35", "xml_views"=>"0", "html_views"=>"247"}
  • {"month"=>"6", "year"=>"2015", "pdf_views"=>"30", "xml_views"=>"0", "html_views"=>"216"}
  • {"month"=>"7", "year"=>"2015", "pdf_views"=>"33", "xml_views"=>"0", "html_views"=>"217"}
  • {"month"=>"8", "year"=>"2015", "pdf_views"=>"30", "xml_views"=>"0", "html_views"=>"237"}
  • {"month"=>"9", "year"=>"2015", "pdf_views"=>"57", "xml_views"=>"1", "html_views"=>"302"}
  • {"month"=>"10", "year"=>"2015", "pdf_views"=>"50", "xml_views"=>"1", "html_views"=>"273"}
  • {"month"=>"11", "year"=>"2015", "pdf_views"=>"21", "xml_views"=>"0", "html_views"=>"266"}
  • {"month"=>"12", "year"=>"2015", "pdf_views"=>"28", "xml_views"=>"0", "html_views"=>"241"}
  • {"month"=>"1", "year"=>"2016", "pdf_views"=>"34", "xml_views"=>"0", "html_views"=>"206"}
  • {"month"=>"2", "year"=>"2016", "pdf_views"=>"35", "xml_views"=>"0", "html_views"=>"262"}
  • {"month"=>"3", "year"=>"2016", "pdf_views"=>"24", "xml_views"=>"0", "html_views"=>"192"}
  • {"month"=>"4", "year"=>"2016", "pdf_views"=>"31", "xml_views"=>"0", "html_views"=>"178"}
  • {"month"=>"5", "year"=>"2016", "pdf_views"=>"32", "xml_views"=>"0", "html_views"=>"259"}
  • {"month"=>"6", "year"=>"2016", "pdf_views"=>"36", "xml_views"=>"0", "html_views"=>"200"}
  • {"month"=>"7", "year"=>"2016", "pdf_views"=>"43", "xml_views"=>"0", "html_views"=>"193"}
  • {"month"=>"8", "year"=>"2016", "pdf_views"=>"35", "xml_views"=>"0", "html_views"=>"216"}
  • {"month"=>"9", "year"=>"2016", "pdf_views"=>"48", "xml_views"=>"0", "html_views"=>"376"}
  • {"month"=>"10", "year"=>"2016", "pdf_views"=>"35", "xml_views"=>"0", "html_views"=>"339"}
  • {"month"=>"11", "year"=>"2016", "pdf_views"=>"13", "xml_views"=>"2", "html_views"=>"356"}
  • {"month"=>"12", "year"=>"2016", "pdf_views"=>"32", "xml_views"=>"4", "html_views"=>"344"}
  • {"month"=>"1", "year"=>"2017", "pdf_views"=>"47", "xml_views"=>"5", "html_views"=>"334"}
  • {"month"=>"2", "year"=>"2017", "pdf_views"=>"49", "xml_views"=>"6", "html_views"=>"319"}
  • {"month"=>"3", "year"=>"2017", "pdf_views"=>"33", "xml_views"=>"4", "html_views"=>"329"}
  • {"month"=>"4", "year"=>"2017", "pdf_views"=>"13", "xml_views"=>"2", "html_views"=>"276"}
  • {"month"=>"5", "year"=>"2017", "pdf_views"=>"33", "xml_views"=>"5", "html_views"=>"322"}
  • {"month"=>"6", "year"=>"2017", "pdf_views"=>"25", "xml_views"=>"2", "html_views"=>"254"}
  • {"month"=>"7", "year"=>"2017", "pdf_views"=>"30", "xml_views"=>"6", "html_views"=>"321"}
  • {"month"=>"8", "year"=>"2017", "pdf_views"=>"30", "xml_views"=>"4", "html_views"=>"292"}
  • {"month"=>"9", "year"=>"2017", "pdf_views"=>"31", "xml_views"=>"2", "html_views"=>"300"}
  • {"month"=>"10", "year"=>"2017", "pdf_views"=>"26", "xml_views"=>"7", "html_views"=>"308"}
  • {"month"=>"11", "year"=>"2017", "pdf_views"=>"26", "xml_views"=>"2", "html_views"=>"378"}
  • {"month"=>"12", "year"=>"2017", "pdf_views"=>"43", "xml_views"=>"1", "html_views"=>"272"}
  • {"month"=>"1", "year"=>"2018", "pdf_views"=>"41", "xml_views"=>"0", "html_views"=>"195"}
  • {"month"=>"2", "year"=>"2018", "pdf_views"=>"28", "xml_views"=>"1", "html_views"=>"100"}
  • {"month"=>"3", "year"=>"2018", "pdf_views"=>"31", "xml_views"=>"1", "html_views"=>"104"}
  • {"month"=>"4", "year"=>"2018", "pdf_views"=>"21", "xml_views"=>"2", "html_views"=>"89"}
  • {"month"=>"5", "year"=>"2018", "pdf_views"=>"32", "xml_views"=>"1", "html_views"=>"117"}
  • {"month"=>"6", "year"=>"2018", "pdf_views"=>"15", "xml_views"=>"1", "html_views"=>"88"}
  • {"month"=>"7", "year"=>"2018", "pdf_views"=>"23", "xml_views"=>"3", "html_views"=>"106"}
  • {"month"=>"8", "year"=>"2018", "pdf_views"=>"24", "xml_views"=>"2", "html_views"=>"91"}
  • {"month"=>"9", "year"=>"2018", "pdf_views"=>"25", "xml_views"=>"0", "html_views"=>"73"}
  • {"month"=>"10", "year"=>"2018", "pdf_views"=>"28", "xml_views"=>"2", "html_views"=>"77"}
  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"27", "xml_views"=>"0", "html_views"=>"96"}
  • {"month"=>"12", "year"=>"2018", "pdf_views"=>"25", "xml_views"=>"0", "html_views"=>"56"}
  • {"month"=>"1", "year"=>"2019", "pdf_views"=>"12", "xml_views"=>"1", "html_views"=>"61"}

Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/773180"], "description"=>"<p>RNA-Seq evidence, annotation information and validation information is shown for each prediction for which validation by PCR was attempted.</p>", "links"=>[], "tags"=>["validated", "defuse"], "article_id"=>443533, "categories"=>["Infectious Diseases", "Cancer"], "users"=>["Andrew McPherson", "Fereydoun Hormozdiari", "Abdalnasser Zayed", "Ryan Giuliany", "Gavin Ha", "Mark G. F. Sun", "Malachi Griffith", "Alireza Heravi Moussavi", "Janine Senz", "Nataliya Melnyk", "Marina Pacheco", "Marco A. Marra", "Martin Hirst", "Torsten O. Nielsen", "S. Cenk Sahinalp", "David Huntsman", "Sohrab P. Shah"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1001138.t002", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_RT_PCR_validated_novel_deFuse_predictions_/443533", "title"=>"RT-PCR validated novel deFuse predictions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-19 00:58:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/772629"], "description"=>"<p><b>a</b>) Discordant alignments are clustered based on the likelihood that those alignments were produced by reads spanning the same fusion boundary. Ambiguous alignments are resolved by selecting the most likely set of fusion events, and the most likely assignment of paired end reads to those events, and the remaining alignments are discarded. <b>b</b>) Paired end reads with an alignment for which one end aligns near the approximate fusion boundary are mined for split alignments of the other end of the read. <b>c</b>) The predicted fusion boundary is used to calculate the fragment lengths for each spanning paired end read. These fragment lengths are tested for the hypothesis that they were drawn at random from the fragment length distribution.</p>", "links"=>[], "tags"=>["defuse", "fusion"], "article_id"=>442979, "categories"=>["Infectious Diseases", "Cancer"], "users"=>["Andrew McPherson", "Fereydoun Hormozdiari", "Abdalnasser Zayed", "Ryan Giuliany", "Gavin Ha", "Mark G. F. Sun", "Malachi Griffith", "Alireza Heravi Moussavi", "Janine Senz", "Nataliya Melnyk", "Marina Pacheco", "Marco A. Marra", "Martin Hirst", "Torsten O. Nielsen", "S. Cenk Sahinalp", "David Huntsman", "Sohrab P. Shah"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1001138.g001", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_deFuse_gene_fusion_discovery_method_/442979", "title"=>"The deFuse gene fusion discovery method.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 00:49:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/772698"], "description"=>"<p><b>a</b>) Fusion transcript X-Y supported by a paired end read spanning the fusion boundary. <b>b</b>) Discordant paired end reads represent reads potentially spanning a fusion boundary. Each discordant alignment suggests fusion boundaries in the regions adjacent to the alignments in each transcript. The <i>fusion boundary region</i>, shown in gray, is the region in which we expect a fusion boundary to occur. <b>c</b>) The <i>overlapping boundary region condition</i> is the condition that the fusion boundary regions in each transcript must overlap. <b>d</b>) The difference between the fragment lengths of two paired end reads spanning a fusion boundary is . <b>e</b>) The <i>similar fragment length condition</i> is the constraint that must be no more than .</p>", "links"=>[], "tags"=>["considering", "paired", "reads", "originated", "fusion"], "article_id"=>443052, "categories"=>["Infectious Diseases", "Cancer"], "users"=>["Andrew McPherson", "Fereydoun Hormozdiari", "Abdalnasser Zayed", "Ryan Giuliany", "Gavin Ha", "Mark G. F. Sun", "Malachi Griffith", "Alireza Heravi Moussavi", "Janine Senz", "Nataliya Melnyk", "Marina Pacheco", "Marco A. Marra", "Martin Hirst", "Torsten O. Nielsen", "S. Cenk Sahinalp", "David Huntsman", "Sohrab P. Shah"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1001138.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conditions_for_considering_two_paired_end_reads_to_have_originated_from_the_same_fusion_transcript_/443052", "title"=>"Conditions for considering two paired end reads to have originated from the same fusion transcript.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 00:50:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/773378"], "description"=>"<p>Results for an analysis of existing datasets using deFuse thresholds and deFuse classifier.</p>", "links"=>[], "tags"=>["predictions", "datasets"], "article_id"=>443731, "categories"=>["Infectious Diseases", "Cancer"], "users"=>["Andrew McPherson", "Fereydoun Hormozdiari", "Abdalnasser Zayed", "Ryan Giuliany", "Gavin Ha", "Mark G. F. Sun", "Malachi Griffith", "Alireza Heravi Moussavi", "Janine Senz", "Nataliya Melnyk", "Marina Pacheco", "Marco A. Marra", "Martin Hirst", "Torsten O. Nielsen", "S. Cenk Sahinalp", "David Huntsman", "Sohrab P. Shah"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1001138.t005", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_deFuse_predictions_for_existing_datasets_with_known_fusions_/443731", "title"=>"deFuse predictions for existing datasets with known fusions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-19 01:02:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/773334"], "description"=>"<p>Comparison of accuracy between deFuse and FusionSeq on a subset of events predicted by either method in CCC15, CCC16 and EMD6. There were 21 PCR validations attempted including 17 positives (P) and 4 negatives (N). TP: true positives, TN: true negatives, FP: false positives, FN: false negatives, Sens = , Spec = .</p>", "links"=>[], "tags"=>["metrics", "fusionseq"], "article_id"=>443683, "categories"=>["Infectious Diseases", "Cancer"], "users"=>["Andrew McPherson", "Fereydoun Hormozdiari", "Abdalnasser Zayed", "Ryan Giuliany", "Gavin Ha", "Mark G. F. Sun", "Malachi Griffith", "Alireza Heravi Moussavi", "Janine Senz", "Nataliya Melnyk", "Marina Pacheco", "Marco A. Marra", "Martin Hirst", "Torsten O. Nielsen", "S. Cenk Sahinalp", "David Huntsman", "Sohrab P. Shah"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1001138.t004", "stats"=>{"downloads"=>4, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_accuracy_metrics_for_FusionSeq_and_deFuse_/443683", "title"=>"Comparison of accuracy metrics for FusionSeq and deFuse.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-19 01:01:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/773014"], "description"=>"<p><b>a</b>) Validation evidence using a FISH come together assay, with fusion probes circled in white. <b>b</b>) FISH probe selection. <b>c</b>) <i>FRYL</i> exonic coverage showing fewer reads aligning after the fusion boundary. <i>FRYL</i> exons in blue with narrower boxes denoting untranslated sequence. <b>d</b>) <i>SH2D1A</i> exonic coverage showing significant coverage after the fusion boundary. <i>SH2D1A</i> exons in green with narrower boxes denoting untranslated sequence. <b>e</b>, <i>FRYL</i>-<i>SH2D1A</i> exons in blue or green depending on their origin, with the whole transcript predicted as untranslated. <b>f</b>) Positions of spanning reads supporting the fusion. <b>g</b>, Split alignments supporting the fusion prediction. <b>h</b>) Chromatogram of a sequenced PCR product supporting the fusion.</p>", "links"=>[], "tags"=>["fusion", "validated"], "article_id"=>443362, "categories"=>["Infectious Diseases", "Cancer"], "users"=>["Andrew McPherson", "Fereydoun Hormozdiari", "Abdalnasser Zayed", "Ryan Giuliany", "Gavin Ha", "Mark G. F. Sun", "Malachi Griffith", "Alireza Heravi Moussavi", "Janine Senz", "Nataliya Melnyk", "Marina Pacheco", "Marco A. Marra", "Martin Hirst", "Torsten O. Nielsen", "S. Cenk Sahinalp", "David Huntsman", "Sohrab P. Shah"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1001138.g006", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evidence_for_the_FRYL_SH2D1A_fusion_showing_the_validated_fusion_boundary_vertical_red_line_/443362", "title"=>"Evidence for the <i>FRYL</i>-<i>SH2D1A</i> fusion showing the validated fusion boundary (vertical red line).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 00:56:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/773117"], "description"=>"<p><b>a</b>) Read depth across <i>HNF1A</i> exonic positions shows that only the region after the fusion boundary is being expressed, evidence of the possible biallelic inactivation of <i>HNF1A</i>. <b>b</b>) Putative <i>RREB1</i>-<i>TFE3</i> chimeric protein showing preservation of <i>TFE3's</i> basic helix-loop-helix (bHLH) leucine zipper (LZ) domain and N-terminal activation domain (ATA), in addition to 4 of <i>RREB1</i>'s zinc finger (ZF) motifs.</p>", "links"=>[], "tags"=>["sarcoma"], "article_id"=>443471, "categories"=>["Infectious Diseases", "Cancer"], "users"=>["Andrew McPherson", "Fereydoun Hormozdiari", "Abdalnasser Zayed", "Ryan Giuliany", "Gavin Ha", "Mark G. F. Sun", "Malachi Griffith", "Alireza Heravi Moussavi", "Janine Senz", "Nataliya Melnyk", "Marina Pacheco", "Marco A. Marra", "Martin Hirst", "Torsten O. Nielsen", "S. Cenk Sahinalp", "David Huntsman", "Sohrab P. Shah"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1001138.g007", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fusions_in_sarcoma_samples_/443471", "title"=>"Fusions in sarcoma samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 00:57:51"}
  • {"files"=>["https://ndownloader.figshare.com/files/772836"], "description"=>"<p>ROC curve for deFuse annotated with the threshold for the adaboost probability estimate. The threshold corresponds to a false positive rate of 10% and true positive rate of 82%.</p>", "links"=>[], "tags"=>["roc"], "article_id"=>443197, "categories"=>["Infectious Diseases", "Cancer"], "users"=>["Andrew McPherson", "Fereydoun Hormozdiari", "Abdalnasser Zayed", "Ryan Giuliany", "Gavin Ha", "Mark G. F. Sun", "Malachi Griffith", "Alireza Heravi Moussavi", "Janine Senz", "Nataliya Melnyk", "Marina Pacheco", "Marco A. Marra", "Martin Hirst", "Torsten O. Nielsen", "S. Cenk Sahinalp", "David Huntsman", "Sohrab P. Shah"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1001138.g004", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_deFuse_ROC_curve_/443197", "title"=>"deFuse ROC curve.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 00:53:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/772933"], "description"=>"<p>Relative importance of each of the 11 features used by deFuse classifier.</p>", "links"=>[], "tags"=>["defuse"], "article_id"=>443289, "categories"=>["Infectious Diseases", "Cancer"], "users"=>["Andrew McPherson", "Fereydoun Hormozdiari", "Abdalnasser Zayed", "Ryan Giuliany", "Gavin Ha", "Mark G. F. Sun", "Malachi Griffith", "Alireza Heravi Moussavi", "Janine Senz", "Nataliya Melnyk", "Marina Pacheco", "Marco A. Marra", "Martin Hirst", "Torsten O. Nielsen", "S. Cenk Sahinalp", "David Huntsman", "Sohrab P. Shah"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1001138.g005", "stats"=>{"downloads"=>0, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variable_importance_plot_for_deFuse_classifier_/443289", "title"=>"Variable importance plot for deFuse classifier.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 00:54:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/388497", "https://ndownloader.figshare.com/files/388516", "https://ndownloader.figshare.com/files/388530", "https://ndownloader.figshare.com/files/388548", "https://ndownloader.figshare.com/files/388567", "https://ndownloader.figshare.com/files/388596", "https://ndownloader.figshare.com/files/388609", "https://ndownloader.figshare.com/files/388646", "https://ndownloader.figshare.com/files/388663", "https://ndownloader.figshare.com/files/388687", "https://ndownloader.figshare.com/files/388698", "https://ndownloader.figshare.com/files/388711", "https://ndownloader.figshare.com/files/388729", "https://ndownloader.figshare.com/files/388738", "https://ndownloader.figshare.com/files/388751"], "description"=>"<div><p>Gene fusions created by somatic genomic rearrangements are known to play an important role in the onset and development of some cancers, such as lymphomas and sarcomas. RNA-Seq (whole transcriptome shotgun sequencing) is proving to be a useful tool for the discovery of novel gene fusions in cancer transcriptomes. However, algorithmic methods for the discovery of gene fusions using RNA-Seq data remain underdeveloped. We have developed deFuse, a novel computational method for fusion discovery in tumor RNA-Seq data. Unlike existing methods that use only unique best-hit alignments and consider only fusion boundaries at the ends of known exons, deFuse considers all alignments and all possible locations for fusion boundaries. As a result, deFuse is able to identify fusion sequences with demonstrably better sensitivity than previous approaches. To increase the specificity of our approach, we curated a list of 60 true positive and 61 true negative fusion sequences (as confirmed by RT-PCR), and have trained an adaboost classifier on 11 novel features of the sequence data. The resulting classifier has an estimated value of 0.91 for the area under the ROC curve. We have used deFuse to discover gene fusions in 40 ovarian tumor samples, one ovarian cancer cell line, and three sarcoma samples. We report herein the first gene fusions discovered in ovarian cancer. We conclude that gene fusions are not infrequent events in ovarian cancer and that these events have the potential to substantially alter the expression patterns of the genes involved; gene fusions should therefore be considered in efforts to comprehensively characterize the mutational profiles of ovarian cancer transcriptomes.</p></div>", "links"=>[], "tags"=>["algorithm", "fusion", "rna-seq"], "article_id"=>136714, "categories"=>["Cancer"], "users"=>["Andrew McPherson", "Fereydoun Hormozdiari", "Abdalnasser Zayed", "Ryan Giuliany", "Gavin Ha", "Mark G. F. Sun", "Malachi Griffith", "Alireza Heravi Moussavi", "Janine Senz", "Nataliya Melnyk", "Marina Pacheco", "Marco A. Marra", "Martin Hirst", "Torsten O. Nielsen", "S. Cenk Sahinalp", "David Huntsman", "Sohrab P. Shah"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1001138.s001", "https://dx.doi.org/10.1371/journal.pcbi.1001138.s002", "https://dx.doi.org/10.1371/journal.pcbi.1001138.s003", "https://dx.doi.org/10.1371/journal.pcbi.1001138.s004", "https://dx.doi.org/10.1371/journal.pcbi.1001138.s005", "https://dx.doi.org/10.1371/journal.pcbi.1001138.s006", "https://dx.doi.org/10.1371/journal.pcbi.1001138.s007", "https://dx.doi.org/10.1371/journal.pcbi.1001138.s008", "https://dx.doi.org/10.1371/journal.pcbi.1001138.s009", "https://dx.doi.org/10.1371/journal.pcbi.1001138.s010", "https://dx.doi.org/10.1371/journal.pcbi.1001138.s011", "https://dx.doi.org/10.1371/journal.pcbi.1001138.s012", "https://dx.doi.org/10.1371/journal.pcbi.1001138.s013", "https://dx.doi.org/10.1371/journal.pcbi.1001138.s014", "https://dx.doi.org/10.1371/journal.pcbi.1001138.s015"], "stats"=>{"downloads"=>6, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/deFuse_An_Algorithm_for_Gene_Fusion_Discovery_in_Tumor_RNA_Seq_Data/136714", "title"=>"deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-05-19 01:51:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/773274"], "description"=>"<p>Summary of RNA-Seq statistics and fusion predictions across all samples. LGS: Low Grade Serous, HGS: High Grade Serous, CCC: Clear cell carcinoma, EMD: Endometrioid tumor, MUC: Mucinous tumor, YKS: Yolk sac tumor, GRC: Granulosa cell tumor, SCH: Small cell hypercalemic, EPS: Epithelioid Sarcoma, IGMS: intermediate grade myofibroblastic sarcoma.</p>", "links"=>[], "tags"=>["rna-seq", "fusion"], "article_id"=>443631, "categories"=>["Infectious Diseases", "Cancer"], "users"=>["Andrew McPherson", "Fereydoun Hormozdiari", "Abdalnasser Zayed", "Ryan Giuliany", "Gavin Ha", "Mark G. F. Sun", "Malachi Griffith", "Alireza Heravi Moussavi", "Janine Senz", "Nataliya Melnyk", "Marina Pacheco", "Marco A. Marra", "Martin Hirst", "Torsten O. Nielsen", "S. Cenk Sahinalp", "David Huntsman", "Sohrab P. Shah"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1001138.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_RNA_Seq_and_fusion_analysis_/443631", "title"=>"Summary of RNA-Seq and fusion analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-19 01:00:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/773229"], "description"=>"<p>Comparison of deFuse using heuristic filters (deFuse thresholds) and deFuse using a classifier (deFuse classifier) with FusionSeq.</p>", "links"=>[], "tags"=>["predictions", "compared", "defuse"], "article_id"=>443585, "categories"=>["Infectious Diseases", "Cancer"], "users"=>["Andrew McPherson", "Fereydoun Hormozdiari", "Abdalnasser Zayed", "Ryan Giuliany", "Gavin Ha", "Mark G. F. Sun", "Malachi Griffith", "Alireza Heravi Moussavi", "Janine Senz", "Nataliya Melnyk", "Marina Pacheco", "Marco A. Marra", "Martin Hirst", "Torsten O. Nielsen", "S. Cenk Sahinalp", "David Huntsman", "Sohrab P. Shah"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1001138.t003", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fusions_predictions_compared_between_deFuse_and_FusionSeq_/443585", "title"=>"Fusions predictions compared between deFuse and FusionSeq.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-05-19 00:59:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/772772"], "description"=>"<p><b>a</b>) Approximate fusion boundaries, shown as dashed rectangles, are the intersection of fusion boundary regions for discordant alignments supporting a potential fusion. <b>b</b>) The mate alignment region, shown as a dashed rectangle, is the union of possible alignment locations for the other end of a single end anchored alignment. <b>c</b>) The approximate fusion boundary in transcript is projected into transcript by remapping the start of the approximate fusion boundary from , to the genome, to .</p>", "links"=>[], "tags"=>["computational biology/genomics", "computer science/applications", "oncology/genitourinary cancers", "oncology/sarcomas"], "article_id"=>443122, "categories"=>["Infectious Diseases", "Cancer"], "users"=>["Andrew McPherson", "Fereydoun Hormozdiari", "Abdalnasser Zayed", "Ryan Giuliany", "Gavin Ha", "Mark G. F. Sun", "Malachi Griffith", "Alireza Heravi Moussavi", "Janine Senz", "Nataliya Melnyk", "Marina Pacheco", "Marco A. Marra", "Martin Hirst", "Torsten O. Nielsen", "S. Cenk Sahinalp", "David Huntsman", "Sohrab P. Shah"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1001138.g003", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Searching_for_candidate_split_reads_/443122", "title"=>"Searching for candidate split reads.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-05-19 00:52:02"}

PMC Usage Stats | Further Information

  • {"month"=>"5", "scanned-page-browse"=>"0", "cited-by"=>"0", "abstract"=>"0", "full-text"=>"8", "year"=>"2011", "pdf"=>"4", "unique-ip"=>"9", "figure"=>"2", "scanned-summary"=>"0", "supp-data"=>"0"}
  • {"scanned-page-browse"=>"0", "month"=>"6", "cited-by"=>"0", "abstract"=>"0", "full-text"=>"135", "unique-ip"=>"130", "pdf"=>"69", "year"=>"2011", "figure"=>"38", "scanned-summary"=>"0", "supp-data"=>"10"}
  • {"month"=>"7", "scanned-page-browse"=>"0", "cited-by"=>"0", "abstract"=>"0", "full-text"=>"66", "year"=>"2011", "pdf"=>"38", "unique-ip"=>"66", "figure"=>"13", "scanned-summary"=>"0", "supp-data"=>"31"}
  • {"scanned-page-browse"=>"0", "month"=>"8", "cited-by"=>"0", "abstract"=>"0", "full-text"=>"67", "unique-ip"=>"64", "pdf"=>"27", "year"=>"2011", "figure"=>"17", "scanned-summary"=>"0", "supp-data"=>"2"}
  • {"month"=>"9", "scanned-page-browse"=>"0", "cited-by"=>"0", "abstract"=>"1", "full-text"=>"68", "year"=>"2011", "pdf"=>"42", "unique-ip"=>"68", "figure"=>"11", "scanned-summary"=>"0", "supp-data"=>"12"}
  • {"scanned-page-browse"=>"0", "month"=>"10", "cited-by"=>"1", "abstract"=>"0", "full-text"=>"66", "unique-ip"=>"63", "pdf"=>"37", "year"=>"2011", "figure"=>"20", "scanned-summary"=>"0", "supp-data"=>"4"}
  • {"month"=>"11", "scanned-page-browse"=>"0", "cited-by"=>"1", "abstract"=>"0", "full-text"=>"46", "year"=>"2011", "pdf"=>"26", "unique-ip"=>"44", "figure"=>"4", "scanned-summary"=>"0", "supp-data"=>"1"}
  • {"scanned-page-browse"=>"0", "month"=>"12", "cited-by"=>"0", "abstract"=>"1", "full-text"=>"44", "unique-ip"=>"43", "pdf"=>"27", "year"=>"2011", "figure"=>"4", "scanned-summary"=>"0", "supp-data"=>"0"}
  • {"scanned-page-browse"=>"0", "month"=>"1", "cited-by"=>"0", "abstract"=>"2", "full-text"=>"50", "unique-ip"=>"39", "pdf"=>"18", "year"=>"2012", "figure"=>"9", "scanned-summary"=>"0", "supp-data"=>"13"}
  • {"month"=>"2", "scanned-page-browse"=>"0", "cited-by"=>"0", "abstract"=>"1", "full-text"=>"45", "year"=>"2012", "pdf"=>"28", "unique-ip"=>"44", "figure"=>"8", "scanned-summary"=>"0", "supp-data"=>"6"}
  • {"scanned-page-browse"=>"0", "month"=>"3", "cited-by"=>"0", "abstract"=>"1", "full-text"=>"49", "unique-ip"=>"41", "pdf"=>"30", "year"=>"2012", "figure"=>"20", "scanned-summary"=>"0", "supp-data"=>"1"}
  • {"month"=>"4", "scanned-page-browse"=>"0", "cited-by"=>"1", "abstract"=>"0", "full-text"=>"79", "year"=>"2012", "pdf"=>"37", "unique-ip"=>"60", "figure"=>"12", "scanned-summary"=>"0", "supp-data"=>"0"}
  • {"scanned-page-browse"=>"0", "month"=>"5", "cited-by"=>"0", "abstract"=>"4", "full-text"=>"36", "unique-ip"=>"35", "pdf"=>"18", "year"=>"2012", "figure"=>"35", "scanned-summary"=>"0", "supp-data"=>"1"}
  • {"month"=>"6", "scanned-page-browse"=>"0", "cited-by"=>"0", "abstract"=>"1", "full-text"=>"53", "year"=>"2012", "pdf"=>"22", "unique-ip"=>"43", "figure"=>"10", "scanned-summary"=>"0", "supp-data"=>"8"}
  • {"unique-ip"=>"48", "full-text"=>"53", "pdf"=>"17", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"18", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2012", "month"=>"7"}
  • {"unique-ip"=>"36", "full-text"=>"33", "pdf"=>"18", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"29", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2012", "month"=>"8"}
  • {"unique-ip"=>"30", "full-text"=>"31", "pdf"=>"13", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"16", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2012", "month"=>"9"}
  • {"unique-ip"=>"45", "full-text"=>"53", "pdf"=>"28", "abstract"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"10", "supp-data"=>"9", "cited-by"=>"0", "year"=>"2012", "month"=>"10"}
  • {"unique-ip"=>"25", "full-text"=>"26", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"15", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2012", "month"=>"12"}
  • {"unique-ip"=>"39", "full-text"=>"40", "pdf"=>"22", "abstract"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2013", "month"=>"1"}
  • {"unique-ip"=>"28", "full-text"=>"30", "pdf"=>"12", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2013", "month"=>"2"}
  • {"unique-ip"=>"32", "full-text"=>"37", "pdf"=>"14", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"21", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2013", "month"=>"3"}
  • {"unique-ip"=>"23", "full-text"=>"29", "pdf"=>"12", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"20", "cited-by"=>"0", "year"=>"2013", "month"=>"4"}
  • {"unique-ip"=>"36", "full-text"=>"33", "pdf"=>"18", "abstract"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"15", "supp-data"=>"3", "cited-by"=>"1", "year"=>"2012", "month"=>"11"}
  • {"unique-ip"=>"30", "full-text"=>"32", "pdf"=>"9", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2013", "month"=>"5"}
  • {"unique-ip"=>"29", "full-text"=>"30", "pdf"=>"17", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2013", "month"=>"6"}
  • {"unique-ip"=>"27", "full-text"=>"27", "pdf"=>"11", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"14", "cited-by"=>"0", "year"=>"2013", "month"=>"7"}
  • {"unique-ip"=>"31", "full-text"=>"31", "pdf"=>"13", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"7", "cited-by"=>"0", "year"=>"2013", "month"=>"8"}
  • {"unique-ip"=>"15", "full-text"=>"17", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"17", "cited-by"=>"0", "year"=>"2013", "month"=>"9"}
  • {"unique-ip"=>"21", "full-text"=>"25", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"1", "cited-by"=>"1", "year"=>"2013", "month"=>"10"}
  • {"unique-ip"=>"27", "full-text"=>"27", "pdf"=>"13", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"25", "supp-data"=>"1", "cited-by"=>"1", "year"=>"2013", "month"=>"11"}
  • {"unique-ip"=>"14", "full-text"=>"17", "pdf"=>"7", "abstract"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2013", "month"=>"12"}
  • {"unique-ip"=>"20", "full-text"=>"21", "pdf"=>"12", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2014", "month"=>"1"}
  • {"unique-ip"=>"27", "full-text"=>"28", "pdf"=>"11", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"7", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2014", "month"=>"2"}
  • {"unique-ip"=>"38", "full-text"=>"42", "pdf"=>"13", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"15", "cited-by"=>"2", "year"=>"2014", "month"=>"3"}
  • {"unique-ip"=>"23", "full-text"=>"21", "pdf"=>"11", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2014", "month"=>"5"}
  • {"unique-ip"=>"32", "full-text"=>"27", "pdf"=>"12", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2014", "month"=>"6"}
  • {"unique-ip"=>"24", "full-text"=>"20", "pdf"=>"9", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2014", "month"=>"4"}
  • {"unique-ip"=>"55", "full-text"=>"40", "pdf"=>"9", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"9", "cited-by"=>"2", "year"=>"2014", "month"=>"7"}
  • {"unique-ip"=>"36", "full-text"=>"26", "pdf"=>"14", "abstract"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2014", "month"=>"8"}
  • {"unique-ip"=>"49", "full-text"=>"34", "pdf"=>"16", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"6", "cited-by"=>"1", "year"=>"2014", "month"=>"9"}
  • {"unique-ip"=>"51", "full-text"=>"34", "pdf"=>"16", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"9", "supp-data"=>"7", "cited-by"=>"1", "year"=>"2014", "month"=>"10"}
  • {"unique-ip"=>"55", "full-text"=>"38", "pdf"=>"19", "abstract"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"6", "cited-by"=>"1", "year"=>"2014", "month"=>"11"}
  • {"unique-ip"=>"49", "full-text"=>"43", "pdf"=>"19", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"15", "cited-by"=>"0", "year"=>"2014", "month"=>"12"}
  • {"unique-ip"=>"41", "full-text"=>"37", "pdf"=>"21", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"2", "cited-by"=>"1", "year"=>"2015", "month"=>"1"}
  • {"unique-ip"=>"32", "full-text"=>"35", "pdf"=>"12", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"14", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2015", "month"=>"2"}
  • {"unique-ip"=>"50", "full-text"=>"52", "pdf"=>"14", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"1", "cited-by"=>"1", "year"=>"2015", "month"=>"3"}
  • {"unique-ip"=>"46", "full-text"=>"52", "pdf"=>"19", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"15", "supp-data"=>"13", "cited-by"=>"1", "year"=>"2015", "month"=>"4"}
  • {"unique-ip"=>"55", "full-text"=>"67", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2015", "month"=>"5"}
  • {"unique-ip"=>"54", "full-text"=>"64", "pdf"=>"36", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"14", "supp-data"=>"9", "cited-by"=>"1", "year"=>"2015", "month"=>"6"}
  • {"unique-ip"=>"40", "full-text"=>"68", "pdf"=>"14", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2015", "month"=>"7"}
  • {"unique-ip"=>"32", "full-text"=>"62", "pdf"=>"17", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2015", "month"=>"8"}
  • {"unique-ip"=>"42", "full-text"=>"55", "pdf"=>"14", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2015", "month"=>"9"}
  • {"unique-ip"=>"41", "full-text"=>"48", "pdf"=>"14", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2015", "month"=>"10"}
  • {"unique-ip"=>"43", "full-text"=>"68", "pdf"=>"12", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"17", "supp-data"=>"10", "cited-by"=>"6", "year"=>"2015", "month"=>"11"}
  • {"unique-ip"=>"42", "full-text"=>"55", "pdf"=>"15", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"10", "cited-by"=>"1", "year"=>"2015", "month"=>"12"}
  • {"unique-ip"=>"25", "full-text"=>"37", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"13", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"1"}
  • {"unique-ip"=>"30", "full-text"=>"32", "pdf"=>"13", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
  • {"unique-ip"=>"34", "full-text"=>"45", "pdf"=>"9", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"1", "cited-by"=>"1", "year"=>"2016", "month"=>"3"}
  • {"unique-ip"=>"39", "full-text"=>"52", "pdf"=>"17", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2016", "month"=>"4"}
  • {"unique-ip"=>"30", "full-text"=>"36", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"5", "cited-by"=>"1", "year"=>"2016", "month"=>"5"}
  • {"unique-ip"=>"24", "full-text"=>"36", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"15", "supp-data"=>"9", "cited-by"=>"0", "year"=>"2016", "month"=>"6"}
  • {"unique-ip"=>"23", "full-text"=>"21", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"7"}
  • {"unique-ip"=>"20", "full-text"=>"23", "pdf"=>"9", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2016", "month"=>"8"}
  • {"unique-ip"=>"17", "full-text"=>"14", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"15", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"9"}
  • {"unique-ip"=>"21", "full-text"=>"20", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"7", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"10"}
  • {"unique-ip"=>"32", "full-text"=>"27", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"29", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"11"}
  • {"unique-ip"=>"13", "full-text"=>"16", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"29", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2016", "month"=>"12"}
  • {"unique-ip"=>"20", "full-text"=>"22", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"1"}
  • {"unique-ip"=>"15", "full-text"=>"18", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2017", "month"=>"2"}
  • {"unique-ip"=>"23", "full-text"=>"33", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"15", "cited-by"=>"0", "year"=>"2017", "month"=>"3"}
  • {"unique-ip"=>"18", "full-text"=>"23", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"4"}
  • {"unique-ip"=>"25", "full-text"=>"25", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2017", "month"=>"5"}
  • {"unique-ip"=>"20", "full-text"=>"19", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"10", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2017", "month"=>"6"}
  • {"unique-ip"=>"28", "full-text"=>"32", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"9", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"7"}
  • {"unique-ip"=>"27", "full-text"=>"30", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
  • {"unique-ip"=>"24", "full-text"=>"23", "pdf"=>"8", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"7", "supp-data"=>"17", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"24", "full-text"=>"31", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"9", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"28", "full-text"=>"33", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"13", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"31", "full-text"=>"65", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"15", "supp-data"=>"20", "cited-by"=>"2", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"28", "full-text"=>"38", "pdf"=>"6", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"8", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"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"=>"2018", "month"=>"2"}
  • {"unique-ip"=>"21", "full-text"=>"31", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"12", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}

Relative Metric

{"start_date"=>"2011-01-01T00:00:00Z", "end_date"=>"2011-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[304, 568, 702, 818, 927, 1027, 1118, 1206, 1285, 1357, 1427, 1500, 1564, 1636, 1705, 1773, 1840, 1909, 1974, 2039, 2106, 2170, 2234, 2296, 2358, 2423, 2484, 2546, 2606, 2673, 2734, 2795, 2857, 2921, 2984, 3046, 3100]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[290, 559, 698, 813, 927, 1028, 1121, 1206, 1289, 1360, 1433, 1501, 1569, 1637, 1707, 1774, 1841, 1911, 1974, 2038, 2103, 2161, 2219, 2280, 2345, 2406, 2466, 2529, 2592, 2654, 2713, 2772, 2835, 2893, 2954, 3020, 3071]}, {"subject_area"=>"/Biology and life sciences/Cell biology", "average_usage"=>[289, 559, 699, 817, 931, 1031, 1127, 1214, 1297, 1370, 1444, 1515, 1584, 1656, 1726, 1797, 1862, 1930, 1996, 2061, 2125, 2190, 2250, 2311, 2373, 2435, 2496, 2563, 2630, 2692, 2760, 2824, 2898, 2960, 3019, 3089, 3143]}, {"subject_area"=>"/Physical sciences/Physics", "average_usage"=>[296, 505, 611, 719, 815, 886, 966, 1040, 1111, 1173, 1227, 1283, 1342, 1400, 1459, 1516, 1572, 1635, 1696, 1752, 1804, 1861, 1919, 1976, 2035, 2093, 2142, 2198, 2256, 2309, 2373, 2433, 2486, 2540, 2594, 2652, 2698]}]}

F1000Prime | Further Information

Loading … Spinner
There are currently no alerts