November 23, 2018 Journal article Open Access

Kuijjer, Marieke Lydia

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  <identifier identifierType="DOI">10.5281/zenodo.1494861</identifier>
  <creators>
    <creator>
      <creatorName>Kuijjer, Marieke Lydia</creatorName>
      <givenName>Marieke Lydia</givenName>
      <familyName>Kuijjer</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-6280-3130</nameIdentifier>
      <affiliation>Centre for Molecular Medicine Norway, University of Oslo</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Gene and pathway mutation scores for 5,805 primary tumors from TCGA</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2018</publicationYear>
  <subjects>
    <subject>somatic mutations</subject>
    <subject>mutations</subject>
    <subject>SAMBAR</subject>
    <subject>de-sparsification</subject>
    <subject>cancer</subject>
    <subject>TCGA</subject>
    <subject>mutation data</subject>
    <subject>mutation scores</subject>
    <subject>pathway mutation scores</subject>
    <subject>biological pathways</subject>
    <subject>gene mutation scores</subject>
    <subject>subtypes</subject>
    <subject>cancer subtypes</subject>
    <subject>pan-cancer</subject>
  </subjects>
  <contributors>
    <contributor contributorType="Researcher">
      <contributorName>Paulson, Joseph Nathaniel</contributorName>
      <givenName>Joseph Nathaniel</givenName>
      <familyName>Paulson</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-8221-7139</nameIdentifier>
      <affiliation>Genentech Inc.</affiliation>
    </contributor>
    <contributor contributorType="Researcher">
      <contributorName>Salzman, Peter</contributorName>
      <givenName>Peter</givenName>
      <familyName>Salzman</familyName>
      <affiliation>Bristol-Myers Squibb</affiliation>
    </contributor>
    <contributor contributorType="Researcher">
      <contributorName>Ding, Wei</contributorName>
      <givenName>Wei</givenName>
      <familyName>Ding</familyName>
      <affiliation>University of Massachusetts Boston</affiliation>
    </contributor>
    <contributor contributorType="Researcher">
      <contributorName>Quackenbush, John</contributorName>
      <givenName>John</givenName>
      <familyName>Quackenbush</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-2702-5879</nameIdentifier>
      <affiliation>Harvard TH Chan School of Public Health</affiliation>
    </contributor>
  </contributors>
  <dates>
    <date dateType="Issued">2018-11-23</date>
  </dates>
  <resourceType resourceTypeGeneral="JournalArticle"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/1494861</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.1038/s41416-018-0109-7</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1494839</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/mkuijjer</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/3.0/legalcode">Creative Commons Attribution 3.0 Unported</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;This dataset contains gene and pathway mutation scores for 5,805 primary tumors from 23 different cancer types from The Cancer Genome Atlas (TCGA).&lt;br&gt;
&lt;br&gt;
Gene 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&amp;#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&amp;#39;s gene set size and the number of times a gene is represented in the complete set of pathways. Please see &lt;a href="https://www.nature.com/articles/s41416-018-0109-7"&gt;our publication&lt;/a&gt; in the &lt;em&gt;British Journal of Cancer&lt;/em&gt; for methodological details.&lt;/p&gt;

&lt;p&gt;In the RData file &amp;quot;TCGA_SAMBAR.RData&amp;quot;, we share the following objects:&lt;/p&gt;

&lt;p&gt;- &lt;strong&gt;gene_scores&lt;/strong&gt;: a 2219 by 5805 numeric matrix including gene (rows) mutation scores for each sample (columns).&lt;/p&gt;

&lt;p&gt;- &lt;strong&gt;pathway_scores&lt;/strong&gt;: a 1066 by 5805 numeric matrix including pathway (rows) mutation scores for each sample (columns).&lt;br&gt;
&lt;br&gt;
The file &amp;quot;sample_tumor_annotation.RData&amp;quot; contains the object:&lt;br&gt;
&lt;br&gt;
- &lt;strong&gt;sample_annotation&lt;/strong&gt;: a 5805 by 2 character matrix including sample names (first column) and the tumor type the sample belongs to (&lt;a href="https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations"&gt;TCGA Study Abbreviations&lt;/a&gt;).&lt;/p&gt;</description>
    <description descriptionType="Other">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.</description>
    <description descriptionType="Other">{"references": ["Kuijjer, Marieke Lydia, et al. Br J Cancer. 2018 May;118(11):1492-1501"]}</description>
  </descriptions>
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