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Gene and pathway mutation scores for 5,805 primary tumors from TCGA

Kuijjer, Marieke Lydia


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{
  "description": "<p>This dataset contains gene and pathway mutation scores for 5,805 primary tumors from 23 different cancer types from The Cancer Genome Atlas (TCGA).<br>\n<br>\nGene mutation scores of 2,219 cancer-associated genes were calculated by normalizing the number of non-silent mutations in a gene (obtained from .maf files from TCGA) by the gene&#39;s length. We used SAMBAR (Subtyping Agglomerated Mutations By Annotation Relations) to calculate pathway mutation scores. In short, SAMBAR takes the sum of mutation scores of all genes belonging to a biological pathway and then corrects these scores for the pathway&#39;s gene set size and the number of times a gene is represented in the complete set of pathways. Please see <a href=\"https://www.nature.com/articles/s41416-018-0109-7\">our publication</a> in the <em>British Journal of Cancer</em> for methodological details.</p>\n\n<p>In the RData file &quot;TCGA_SAMBAR.RData&quot;, we share the following objects:</p>\n\n<p>- <strong>gene_scores</strong>: a 2219 by 5805 numeric matrix including gene (rows) mutation scores for each sample (columns).</p>\n\n<p>- <strong>pathway_scores</strong>: a 1066 by 5805 numeric matrix including pathway (rows) mutation scores for each sample (columns).<br>\n<br>\nThe file &quot;sample_tumor_annotation.RData&quot; contains the object:<br>\n<br>\n- <strong>sample_annotation</strong>: a 5805 by 2 character matrix including sample names (first column) and the tumor type the sample belongs to (<a href=\"https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations\">TCGA Study Abbreviations</a>).</p>", 
  "license": "https://creativecommons.org/licenses/by/3.0/legalcode", 
  "creator": [
    {
      "affiliation": "Centre for Molecular Medicine Norway, University of Oslo", 
      "@id": "https://orcid.org/0000-0001-6280-3130", 
      "@type": "Person", 
      "name": "Kuijjer, Marieke Lydia"
    }
  ], 
  "headline": "Gene and pathway mutation scores for 5,805 primary tumors from TCGA", 
  "image": "https://zenodo.org/static/img/logos/zenodo-gradient-round.svg", 
  "citation": [
    {
      "@id": "https://doi.org/10.1038/s41416-018-0109-7", 
      "@type": "CreativeWork"
    }
  ], 
  "datePublished": "2018-11-23", 
  "keywords": [
    "somatic mutations", 
    "mutations", 
    "SAMBAR", 
    "de-sparsification", 
    "cancer", 
    "TCGA", 
    "mutation data", 
    "mutation scores", 
    "pathway mutation scores", 
    "biological pathways", 
    "gene mutation scores", 
    "subtypes", 
    "cancer subtypes", 
    "pan-cancer"
  ], 
  "url": "https://zenodo.org/record/1494861", 
  "contributor": [
    {
      "affiliation": "Genentech Inc.", 
      "@id": "https://orcid.org/0000-0001-8221-7139", 
      "@type": "Person", 
      "name": "Paulson, Joseph Nathaniel"
    }, 
    {
      "affiliation": "Bristol-Myers Squibb", 
      "@type": "Person", 
      "name": "Salzman, Peter"
    }, 
    {
      "affiliation": "University of Massachusetts Boston", 
      "@type": "Person", 
      "name": "Ding, Wei"
    }, 
    {
      "affiliation": "Harvard TH Chan School of Public Health", 
      "@id": "https://orcid.org/0000-0002-2702-5879", 
      "@type": "Person", 
      "name": "Quackenbush, John"
    }
  ], 
  "@context": "https://schema.org/", 
  "identifier": "https://doi.org/10.5281/zenodo.1494861", 
  "@id": "https://doi.org/10.5281/zenodo.1494861", 
  "@type": "ScholarlyArticle", 
  "name": "Gene and pathway mutation scores for 5,805 primary tumors from TCGA"
}
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