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Research Article

Network-Guided Analysis of Genes with Altered Somatic Copy Number and Gene Expression Reveals Pathways Commonly Perturbed in Metastatic Melanoma

  • Armand Valsesia,

    Affiliations: Ludwig Institute for Cancer Research, Lausanne, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland, Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland

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  • Donata Rimoldi,

    Affiliation: Ludwig Institute for Cancer Research, Lausanne, Switzerland

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  • Danielle Martinet,

    Affiliation: Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland

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  • Mark Ibberson,

    Affiliation: Swiss Institute of Bioinformatics, Lausanne, Switzerland

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  • Paola Benaglio,

    Affiliation: Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland

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  • Manfredo Quadroni,

    Affiliation: Protein Analysis Facility, Center for Integrative Genomics, Lausanne, Switzerland

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  • Patrice Waridel,

    Affiliation: Protein Analysis Facility, Center for Integrative Genomics, Lausanne, Switzerland

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  • Muriel Gaillard,

    Affiliation: Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland

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  • Mireille Pidoux,

    Affiliation: Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland

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  • Blandine Rapin,

    Affiliation: Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland

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  • Carlo Rivolta,

    Affiliation: Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland

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  • Ioannis Xenarios,

    Affiliation: Swiss Institute of Bioinformatics, Lausanne, Switzerland

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  • Andrew J. G. Simpson,

    Affiliation: Ludwig Institute for Cancer Research, New York, New York, United States of America

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  • Stylianos E. Antonarakis,

    Affiliation: Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland

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  • Jacques S. Beckmann,

    Affiliations: Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland, Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland

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  • C. Victor Jongeneel,

    Affiliations: Ludwig Institute for Cancer Research, Lausanne, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland, Institute for Genomic Biology and National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America

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  • Christian Iseli mail,

    Christian.Iseli@unil.ch (CI); Brian.Stevenson@unil.ch (BJS)

    Affiliations: Ludwig Institute for Cancer Research, Lausanne, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland

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  • Brian J. Stevenson mail

    Christian.Iseli@unil.ch (CI); Brian.Stevenson@unil.ch (BJS)

    Affiliations: Ludwig Institute for Cancer Research, Lausanne, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland

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  • Published: April 08, 2011
  • DOI: 10.1371/journal.pone.0018369

About the Authors

Armand Valsesia, Donata Rimoldi, C. Victor Jongeneel, Christian Iseli, Brian J. Stevenson
Ludwig Institute for Cancer Research, Lausanne, Switzerland
Armand Valsesia, Mark Ibberson, Ioannis Xenarios, C. Victor Jongeneel, Christian Iseli, Brian J. Stevenson
Swiss Institute of Bioinformatics, Lausanne, Switzerland
Armand Valsesia, Paola Benaglio, Carlo Rivolta, Jacques S. Beckmann
Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
Danielle Martinet, Muriel Gaillard, Mireille Pidoux, Blandine Rapin, Jacques S. Beckmann
Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
Manfredo Quadroni, Patrice Waridel
Protein Analysis Facility, Center for Integrative Genomics, Lausanne, Switzerland
Andrew J. G. Simpson
Ludwig Institute for Cancer Research, New York, New York, United States of America
Stylianos E. Antonarakis
Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
C. Victor Jongeneel
Institute for Genomic Biology and National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America

Corresponding Authors

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: AV AJGS BJS CI CVJ DR JSB SEA. Performed the experiments: BR DM DR MG MP MQ PB PW. Analyzed the data: AV CI MI MQ PW. Wrote the paper: AV BJS CVJ DR. Provided expertise for the Network-guided analysis: IX. Supervised CGH experiments: DM JSB. Supervised SNP experiments: CR. Interpreted the data: AV BJS DR.