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Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC

Gruber, Andreas J.; Schmidt, Ralf; Ghosh, Souvik; Martin, Georges; Gruber, Andreas R.; van Nimwegen, Erik; Zavolan, Mihaela


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  <identifier identifierType="DOI">10.5281/zenodo.1147433</identifier>
  <creators>
    <creator>
      <creatorName>Gruber, Andreas J.</creatorName>
      <givenName>Andreas J.</givenName>
      <familyName>Gruber</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-7664-4257</nameIdentifier>
      <affiliation>Computational and Systems Biology, Biozentrum, University of Basel</affiliation>
    </creator>
    <creator>
      <creatorName>Schmidt, Ralf</creatorName>
      <givenName>Ralf</givenName>
      <familyName>Schmidt</familyName>
      <affiliation>Computational and Systems Biology, Biozentrum, University of Basel</affiliation>
    </creator>
    <creator>
      <creatorName>Ghosh, Souvik</creatorName>
      <givenName>Souvik</givenName>
      <familyName>Ghosh</familyName>
      <affiliation>Computational and Systems Biology, Biozentrum, University of Basel</affiliation>
    </creator>
    <creator>
      <creatorName>Martin, Georges</creatorName>
      <givenName>Georges</givenName>
      <familyName>Martin</familyName>
      <affiliation>Computational and Systems Biology, Biozentrum, University of Basel</affiliation>
    </creator>
    <creator>
      <creatorName>Gruber, Andreas R.</creatorName>
      <givenName>Andreas R.</givenName>
      <familyName>Gruber</familyName>
      <affiliation>Computational and Systems Biology, Biozentrum, University of Basel</affiliation>
    </creator>
    <creator>
      <creatorName>van Nimwegen, Erik</creatorName>
      <givenName>Erik</givenName>
      <familyName>van Nimwegen</familyName>
      <affiliation>Computational and Systems Biology, Biozentrum, University of Basel</affiliation>
    </creator>
    <creator>
      <creatorName>Zavolan, Mihaela</creatorName>
      <givenName>Mihaela</givenName>
      <familyName>Zavolan</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-8832-2041</nameIdentifier>
      <affiliation>Computational and Systems Biology, Biozentrum, University of Basel</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2018</publicationYear>
  <subjects>
    <subject>Cleavage and polyadenylation</subject>
    <subject>APA</subject>
    <subject>quantification of poly(A) site usage</subject>
    <subject>regulators of polyadenylation</subject>
    <subject>HNRNPC</subject>
    <subject>RNA-seq</subject>
    <subject>Snakemake</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2018-01-15</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Software"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/1147433</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">10.1101/195958</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.1147432</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://opensource.org/licenses/GPL-2.0">GNU General Public License v2.0 only</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;This archive contains the Snakemake workflow as it was used in the Genome Biology publication. The workflow is provided in a self-contained environment that only requires Conda and Snakemake to be executed.&amp;nbsp;It&amp;nbsp;connects the PAQR and KAPAC modules and includes as example&amp;nbsp;input the&amp;nbsp;mapped RNA-seq samples from the study of HNRNPC knock-down in HEK293 cells (originally published on the GEO database with the accession number&amp;nbsp;GSE56010), available also from here:&amp;nbsp;http://www.clipz.unibas.ch/RNAseq_HNRNPC_KD_study.&amp;nbsp;&lt;/p&gt;

&lt;p&gt;PAQR is&amp;nbsp;a method for polyadenylation site usage quantification from RNA sequencing data. KAPAC&amp;nbsp;infers position-dependent activities of sequence motifs on 3&amp;rsquo; end processing from changes in poly(A) site usage between conditions.&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100001711</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/SNSF/Programmes/51NF40_141735/">51NF40_141735</awardNumber>
      <awardTitle>NCCR RNA &amp;amp; disease: Understanding the role of RNA biology in disease mechanisms (phase I)</awardTitle>
    </fundingReference>
    <fundingReference>
      <funderName>Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100001711</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/SNSF/Project+funding/31003A_170216/">31003A_170216</awardNumber>
      <awardTitle>Regulation of mRNA translation and its relationship with disease processes</awardTitle>
    </fundingReference>
  </fundingReferences>
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