Preprint Open Access

Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases

Ravel, Jean-Marie; Monraz Gomec, Cristobel L.; Sompairac, Nicolas; Calzone, Laurence; Zhivotovsky, Boris; Kroemer, Guido; Barillot, Emmanuel; Zinovyev, Andrei; Kuperstein, Inna


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  <identifier identifierType="URL">https://zenodo.org/record/3958634</identifier>
  <creators>
    <creator>
      <creatorName>Ravel, Jean-Marie</creatorName>
      <givenName>Jean-Marie</givenName>
      <familyName>Ravel</familyName>
      <affiliation>Institut Curie</affiliation>
    </creator>
    <creator>
      <creatorName>Monraz Gomec, Cristobel L.</creatorName>
      <givenName>Cristobel L.</givenName>
      <familyName>Monraz Gomec</familyName>
      <affiliation>Institut Curie</affiliation>
    </creator>
    <creator>
      <creatorName>Sompairac, Nicolas</creatorName>
      <givenName>Nicolas</givenName>
      <familyName>Sompairac</familyName>
      <affiliation>Institut Curie</affiliation>
    </creator>
    <creator>
      <creatorName>Calzone, Laurence</creatorName>
      <givenName>Laurence</givenName>
      <familyName>Calzone</familyName>
      <affiliation>Institut Curie</affiliation>
    </creator>
    <creator>
      <creatorName>Zhivotovsky, Boris</creatorName>
      <givenName>Boris</givenName>
      <familyName>Zhivotovsky</familyName>
    </creator>
    <creator>
      <creatorName>Kroemer, Guido</creatorName>
      <givenName>Guido</givenName>
      <familyName>Kroemer</familyName>
    </creator>
    <creator>
      <creatorName>Barillot, Emmanuel</creatorName>
      <givenName>Emmanuel</givenName>
      <familyName>Barillot</familyName>
      <affiliation>Institut Curie</affiliation>
    </creator>
    <creator>
      <creatorName>Zinovyev, Andrei</creatorName>
      <givenName>Andrei</givenName>
      <familyName>Zinovyev</familyName>
      <affiliation>Institut Curie</affiliation>
    </creator>
    <creator>
      <creatorName>Kuperstein, Inna</creatorName>
      <givenName>Inna</givenName>
      <familyName>Kuperstein</familyName>
      <affiliation>Institut Curie</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>Regulated cell death</subject>
    <subject>modes of cell death</subject>
    <subject>survival</subject>
    <subject>apoptosis</subject>
    <subject>necroptosis</subject>
    <subject>autophagy</subject>
    <subject>ferropthosis</subject>
    <subject>parthanatos</subject>
    <subject>pyroptosis</subject>
    <subject>signalling network</subject>
    <subject>comprehensive map</subject>
    <subject>process description diagram</subject>
    <subject>pathways</subject>
    <subject>biocuration</subject>
    <subject>NaviCell</subject>
    <subject>MINERVA</subject>
    <subject>NDEx</subject>
    <subject>data visualization</subject>
    <subject>enrichement analysis</subject>
    <subject>module activity</subject>
    <subject>lung cancer</subject>
    <subject>Alzheimer's disease</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-04-17</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Preprint"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3958634</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.3390/cancers12040990</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/ipc</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;The processes leading to, or avoiding cell death are widely studied, because of their frequent perturbation in various diseases. Cell death occurs in three highly interconnected steps: Initiation, signaling and execution. We used a systems biology approach to gather information about all known modes of regulated cell death (RCD). Based on the experimental data retrieved from literature by manual curation, we graphically depicted the biological processes involved in RCD in the form of a seamless comprehensive signaling network map. The molecular mechanisms of each RCD mode are represented in detail. The RCD network map is divided into 26 functional modules that can be visualized contextually in the whole seamless network, as well as in individual diagrams. The resource is freely available and accessible via several web platforms for map navigation, data integration, and analysis. The RCD network map was employed for interpreting the functional differences in cell death regulation between Alzheimer&amp;rsquo;s disease and non-small cell lung cancer based on gene expression data that allowed emphasizing the molecular mechanisms underlying the inverse comorbidity between the two pathologies. In addition, the map was used for the analysis of genomic and transcriptomic data from ovarian cancer patients that provided RCD map-based signatures of four distinct tumor subtypes and highlighted the difference in regulations of cell death molecular mechanisms.&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/H2020/826121/">826121</awardNumber>
      <awardTitle>individualizedPaediatricCure: Cloud-based virtual-patient models for precision paediatric oncology</awardTitle>
    </fundingReference>
  </fundingReferences>
</resource>
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