Exploratory Analysis of the Copy Number Alterations in Glioblastoma Multiforme
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Mendeley | Further Information

{"title"=>"Exploratory Analysis of the Copy Number Alterations in Glioblastoma Multiforme", "type"=>"journal", "authors"=>[{"first_name"=>"Pablo", "last_name"=>"Freire"}, {"first_name"=>"Marco", "last_name"=>"Vilela"}, {"first_name"=>"Helena", "last_name"=>"Deus"}, {"first_name"=>"Yong-Wan", "last_name"=>"Kim"}, {"first_name"=>"Dimpy", "last_name"=>"Koul"}, {"first_name"=>"Howard", "last_name"=>"Colman"}, {"first_name"=>"Kenneth D.", "last_name"=>"Aldape"}, {"first_name"=>"Oliver", "last_name"=>"Bogler"}, {"first_name"=>"W. K. Alfred", "last_name"=>"Yung"}, {"first_name"=>"Kevin", "last_name"=>"Coombes"}, {"first_name"=>"Gordon B.", "last_name"=>"Mills"}, {"first_name"=>"Ana T.", "last_name"=>"Vasconcelos"}, {"first_name"=>"Jonas S.", "last_name"=>"Almeida"}], "year"=>2008, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"354030431", "sgr"=>"58149204044", "issn"=>"1932-6203", "pmid"=>"19115005", "scopus"=>"2-s2.0-58149204044", "doi"=>"10.1371/journal.pone.0004076", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"86a92d39-d8a6-34c5-badf-c2df77f37192", "abstract"=>"BACKGROUND: The Cancer Genome Atlas project (TCGA) has initiated the analysis of multiple samples of a variety of tumor types, starting with glioblastoma multiforme. The analytical methods encompass genomic and transcriptomic information, as well as demographic and clinical data about the sample donors. The data create the opportunity for a systematic screening of the components of the molecular machinery for features that may be associated with tumor formation. The wealth of existing mechanistic information about cancer cell biology provides a natural reference for the exploratory exercise. METHODOLOGY/PRINCIPAL FINDINGS: Glioblastoma multiforme DNA copy number data was generated by The Cancer Genome Atlas project for 167 patients using 227 aCGH experiments, and was analyzed to build a catalog of aberrant regions. Genome screening was performed using an information theory approach in order to quantify aberration as a deviation from a centrality without the bias of untested assumptions about its parametric nature. A novel Cancer Genome Browser software application was developed and is made public to provide a user-friendly graphical interface in which the reported results can be reproduced. The application source code and stand alone executable are available at (http://code.google.com/p/cancergenome) and (http://bioinformaticstation.org), respectively. CONCLUSIONS/SIGNIFICANCE: The most important known copy number alterations for glioblastoma were correctly recovered using entropy as a measure of aberration. Additional alterations were identified in different pathways, such as cell proliferation, cell junctions and neural development. Moreover, novel candidates for oncogenes and tumor suppressors were also detected. A detailed map of aberrant regions is provided.", "link"=>"http://www.mendeley.com/research/exploratory-analysis-copy-number-alterations-glioblastoma-multiforme-9", "reader_count"=>43, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>15, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>9, "Student > Master"=>7, "Other"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>4, "Researcher"=>15, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>9, "Student > Master"=>7, "Other"=>3, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>2, "Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Mathematics"=>1, "Agricultural and Biological Sciences"=>23, "Medicine and Dentistry"=>8, "Neuroscience"=>2, "Computer Science"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>2}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>8}, "Neuroscience"=>{"Neuroscience"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>23}, "Computer Science"=>{"Computer Science"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"South Korea"=>1, "United States"=>4, "Japan"=>1, "United Kingdom"=>1, "India"=>1}, "group_count"=>3}

Scopus | Further Information

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  • {"files"=>["https://ndownloader.figshare.com/files/913082"], "description"=>"<p>Aberrant regions determined by the entropy method. These tables do not include regions for which more then half of the DNA probes were annotated as normal CNV. Candidate oncogenes / suppressors were selected by their potential association with cancer based on their molecular function or for being the only gene in the region. The genomic mapping was based on Build 18. The calling for amplifications and deletions was made by observing which amplitude measure, QQ0.025 (deletion) or 1-QQ0.975 (amplification), was closer to 0.</p>*<p>Not described or validated as oncogene or tumor suppressor in previous studies.</p>", "links"=>[], "tags"=>["deletions", "gbm"], "article_id"=>583527, "categories"=>["Genetics", "Infectious Diseases"], "users"=>["Pablo Freire", "Marco Vilela", "Helena Deus", "Yong-Wan Kim", "Dimpy Koul", "Howard Colman", "Kenneth D. Aldape", "Oliver Bogler", "W. K. Alfred Yung", "Kevin Coombes", "Gordon B. Mills", "Ana T. Vasconcelos", "Jonas S. Almeida"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004076.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Amplifications_and_deletions_in_the_GBM_data_/583527", "title"=>"Amplifications and deletions in the GBM data.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-12-30 00:58:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/450889", "https://ndownloader.figshare.com/files/450922", "https://ndownloader.figshare.com/files/450955", "https://ndownloader.figshare.com/files/450977", "https://ndownloader.figshare.com/files/451005", "https://ndownloader.figshare.com/files/451030", "https://ndownloader.figshare.com/files/451062", "https://ndownloader.figshare.com/files/451093", "https://ndownloader.figshare.com/files/451131", "https://ndownloader.figshare.com/files/451158", "https://ndownloader.figshare.com/files/451193", "https://ndownloader.figshare.com/files/451228", "https://ndownloader.figshare.com/files/451263", "https://ndownloader.figshare.com/files/451288", "https://ndownloader.figshare.com/files/451318", "https://ndownloader.figshare.com/files/451355", "https://ndownloader.figshare.com/files/451376", "https://ndownloader.figshare.com/files/451412", "https://ndownloader.figshare.com/files/451446", "https://ndownloader.figshare.com/files/451475", "https://ndownloader.figshare.com/files/451495", "https://ndownloader.figshare.com/files/451533", "https://ndownloader.figshare.com/files/451567", "https://ndownloader.figshare.com/files/451595", "https://ndownloader.figshare.com/files/451609", "https://ndownloader.figshare.com/files/451631"], "description"=>"<div><h3>Background</h3><p>The Cancer Genome Atlas project (TCGA) has initiated the analysis of multiple samples of a variety of tumor types, starting with glioblastoma multiforme. The analytical methods encompass genomic and transcriptomic information, as well as demographic and clinical data about the sample donors. The data create the opportunity for a systematic screening of the components of the molecular machinery for features that may be associated with tumor formation. The wealth of existing mechanistic information about cancer cell biology provides a natural reference for the exploratory exercise.</p><h3>Methodology/Principal Findings</h3><p>Glioblastoma multiforme DNA copy number data was generated by The Cancer Genome Atlas project for 167 patients using 227 aCGH experiments, and was analyzed to build a catalog of aberrant regions. Genome screening was performed using an information theory approach in order to quantify aberration as a deviation from a centrality without the bias of untested assumptions about its parametric nature. A novel Cancer Genome Browser software application was developed and is made public to provide a user-friendly graphical interface in which the reported results can be reproduced. The application source code and stand alone executable are available at <a href=\"http://code.google.com/p/cancergenome\">http://code.google.com/p/cancergenome</a> and <a href=\"http://bioinformaticstation.org\">http://bioinformaticstation.org</a>, respectively.</p><h3>Conclusions/Significance</h3><p>The most important known copy number alterations for glioblastoma were correctly recovered using entropy as a measure of aberration. Additional alterations were identified in different pathways, such as cell proliferation, cell junctions and neural development. Moreover, novel candidates for oncogenes and tumor suppressors were also detected. A detailed map of aberrant regions is provided.</p></div>", "links"=>[], "tags"=>["exploratory", "alterations", "glioblastoma", "multiforme"], "article_id"=>148867, "categories"=>["Genetics", "Cancer"], "users"=>["Pablo Freire", "Marco Vilela", "Helena Deus", "Yong-Wan Kim", "Dimpy Koul", "Howard Colman", "Kenneth D. Aldape", "Oliver Bogler", "W. K. Alfred Yung", "Kevin Coombes", "Gordon B. Mills", "Ana T. Vasconcelos", "Jonas S. Almeida"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0004076.s001", "https://dx.doi.org/10.1371/journal.pone.0004076.s002", "https://dx.doi.org/10.1371/journal.pone.0004076.s003", "https://dx.doi.org/10.1371/journal.pone.0004076.s004", "https://dx.doi.org/10.1371/journal.pone.0004076.s005", "https://dx.doi.org/10.1371/journal.pone.0004076.s006", "https://dx.doi.org/10.1371/journal.pone.0004076.s007", "https://dx.doi.org/10.1371/journal.pone.0004076.s008", "https://dx.doi.org/10.1371/journal.pone.0004076.s009", "https://dx.doi.org/10.1371/journal.pone.0004076.s010", "https://dx.doi.org/10.1371/journal.pone.0004076.s011", "https://dx.doi.org/10.1371/journal.pone.0004076.s012", "https://dx.doi.org/10.1371/journal.pone.0004076.s013", "https://dx.doi.org/10.1371/journal.pone.0004076.s014", "https://dx.doi.org/10.1371/journal.pone.0004076.s015", "https://dx.doi.org/10.1371/journal.pone.0004076.s016", "https://dx.doi.org/10.1371/journal.pone.0004076.s017", "https://dx.doi.org/10.1371/journal.pone.0004076.s018", "https://dx.doi.org/10.1371/journal.pone.0004076.s019", "https://dx.doi.org/10.1371/journal.pone.0004076.s020", "https://dx.doi.org/10.1371/journal.pone.0004076.s021", "https://dx.doi.org/10.1371/journal.pone.0004076.s022", "https://dx.doi.org/10.1371/journal.pone.0004076.s023", "https://dx.doi.org/10.1371/journal.pone.0004076.s024", "https://dx.doi.org/10.1371/journal.pone.0004076.s025", "https://dx.doi.org/10.1371/journal.pone.0004076.s026"], "stats"=>{"downloads"=>4, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Exploratory_Analysis_of_the_Copy_Number_Alterations_in_Glioblastoma_Multiforme/148867", "title"=>"Exploratory Analysis of the Copy Number Alterations in Glioblastoma Multiforme", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-12-30 02:27:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/912554"], "description"=>"<p>An area under the ROC curve of 1 means a perfect separation between mutated and normal regions, while a value of 0.5 means a random classification.</p>", "links"=>[], "tags"=>["entropy", "roc", "simulated", "accessing", "amplitudes", "prevalences"], "article_id"=>582996, "categories"=>["Genetics", "Infectious Diseases"], "users"=>["Pablo Freire", "Marco Vilela", "Helena Deus", "Yong-Wan Kim", "Dimpy Koul", "Howard Colman", "Kenneth D. Aldape", "Oliver Bogler", "W. K. Alfred Yung", "Kevin Coombes", "Gordon B. Mills", "Ana T. Vasconcelos", "Jonas S. Almeida"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004076.g001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Evaluation_of_the_entropy_method_performance_by_the_area_under_the_ROC_curve_from_simulated_datasets_accessing_different_amplitudes_and_prevalences_of_copy_number_aberrations_/582996", "title"=>"Evaluation of the entropy method performance by the area under the ROC curve from simulated datasets, accessing different amplitudes and prevalences of copy number aberrations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-30 00:49:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/913021"], "description"=>"<p>The values in the diagonal line correspond to variations similarly observed in tumor and normal tissue. The values in the horizontal line correspond to amplifications (right) and deletions (left) observed only in the tumor samples.</p>", "links"=>[], "tags"=>["58", "tumor-normal"], "article_id"=>583470, "categories"=>["Genetics", "Infectious Diseases"], "users"=>["Pablo Freire", "Marco Vilela", "Helena Deus", "Yong-Wan Kim", "Dimpy Koul", "Howard Colman", "Kenneth D. Aldape", "Oliver Bogler", "W. K. Alfred Yung", "Kevin Coombes", "Gordon B. Mills", "Ana T. Vasconcelos", "Jonas S. Almeida"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004076.g004", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Log2_ratio_of_copy_number_of_the_58_tumor_normal_sample_pairs_/583470", "title"=>"Log2 ratio of copy number of the 58 tumor-normal sample pairs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-30 00:57:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/912879"], "description"=>"<p>The prevalence measure adopted is the proportion of DNA probes on determined regions that have a log2 ratio above or below the 0.025 and 0.975 quantiles.</p>", "links"=>[], "tags"=>["prevalence", "entropy", "deletions", "amplifications"], "article_id"=>583321, "categories"=>["Genetics", "Infectious Diseases"], "users"=>["Pablo Freire", "Marco Vilela", "Helena Deus", "Yong-Wan Kim", "Dimpy Koul", "Howard Colman", "Kenneth D. Aldape", "Oliver Bogler", "W. K. Alfred Yung", "Kevin Coombes", "Gordon B. Mills", "Ana T. Vasconcelos", "Jonas S. Almeida"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004076.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Interplay_between_the_amplitude_prevalence_and_entropy_in_deletions_A_and_amplifications_B_/583321", "title"=>"Interplay between the amplitude, prevalence and entropy in deletions (A) and amplifications (B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-30 00:55:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/912714"], "description"=>"<p>The segmented copy number values per sample are displayed as a heatmap on the left, with the tumor samples as columns; the entropy values are shown on the right. The gaps on the heatmap indicate genomic regions that lack coverage, such as the p arms of acrocentric chromosomes. The number in A corresponds to the region number in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004076#pone-0004076-t001\" target=\"_blank\">Table 1</a>. Beside each region label, a plus sign indicates an amplification and a minus indicates a deletion. Note that a low-entropy region can be either a amplification or a deletion. The red line in the entropy plot shows the threshold for defining an aberrant region, which is the 0.05 quantile of the bootstrap distribution of the entropy. Peaks that are below the threshold but have no region assigned are normal CNV. The cytoband annotation was retrieved using the UCSC Table Browser.</p>", "links"=>[], "tags"=>["gbm", "genome", "chromosome"], "article_id"=>583160, "categories"=>["Genetics", "Infectious Diseases"], "users"=>["Pablo Freire", "Marco Vilela", "Helena Deus", "Yong-Wan Kim", "Dimpy Koul", "Howard Colman", "Kenneth D. Aldape", "Oliver Bogler", "W. K. Alfred Yung", "Kevin Coombes", "Gordon B. Mills", "Ana T. Vasconcelos", "Jonas S. Almeida"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004076.g002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Entropy_analysis_for_the_GBM_data_entire_genome_A_chromosome_1_B_and_chromosome_7_C_/583160", "title"=>"Entropy analysis for the GBM data entire genome (A), chromosome 1(B) and chromosome 7 (C).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-12-30 00:52:40"}

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  • {"unique-ip"=>"10", "full-text"=>"11", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"19", "full-text"=>"16", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"14", "full-text"=>"18", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"10", "full-text"=>"10", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"10", "full-text"=>"11", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"15", "full-text"=>"14", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"9", "full-text"=>"6", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"28", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}

Relative Metric

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