Journal article Open Access

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

Kuijjer, Marieke Lydia


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{
  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.1494861", 
  "container_title": "British Journal of Cancer", 
  "title": "Gene and pathway mutation scores for 5,805 primary tumors from TCGA", 
  "issued": {
    "date-parts": [
      [
        2018, 
        11, 
        23
      ]
    ]
  }, 
  "abstract": "<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>", 
  "author": [
    {
      "family": "Kuijjer, Marieke Lydia"
    }
  ], 
  "page": "1492-1501", 
  "volume": "118", 
  "note": "This work was funded through a grant from the NVIDIA foundation (grant no. 2014-133322 (3953)). This work was additionally supported by a Postdoctoral Fellowship Program from the Charles A. King Trust Fund, Sara Elizabeth O'Brien Trust, Bank of America, N.A., co-Trustees.", 
  "type": "article-journal", 
  "issue": "11", 
  "id": "1494861"
}
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