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Pathway and network analysis of cancer genomes

Nature Methods volume 12, pages 615–621 (2015)Cite this article

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Abstract

Genomic information on tumors from 50 cancer types cataloged by the International Cancer Genome Consortium (ICGC) shows that only a few well-studied driver genes are frequently mutated, in contrast to many infrequently mutated genes that may also contribute to tumor biology. Hence there has been large interest in developing pathway and network analysis methods that group genes and illuminate the processes involved. We provide an overview of these analysis techniques and show where they guide mechanistic and translational investigations.

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Figure 1: Major approaches to pathway and network analysis of cancer data.
Figure 2: Pathway and network representations of EGF signaling.

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Acknowledgements

We gratefully acknowledge the assistance of J. Jennings during preparation of this manuscript. J.M.S. acknowledges support from the US National Cancer Institute (R01-CA180778 and U24-CA143858), Stand Up To Cancer, the Prostate Cancer Foundation and the Movember Foundation. P.C. is currently funded by a Ludwig Fund Postdoctoral Fellowship. P.C.B. and L.D.S. were supported by the Ontario Institute for Cancer Research through funding provided by the Government of Ontario. P.C.B. was also supported by a Terry Fox Research Institute New Investigator Award and a Canadian Institutes of Health Research New Investigator Award. L.D.S. and G.W. acknowledge support from the US National Institutes of Health (NIH) and National Human Genome Research Institute (P41 HG003751). G.D.B. is supported by NRNB (NIH, National Institute of General Medical Sciences grant number P41 GM103504).

Author information

Author notes

  1. Pau Creixell

    Present address: Present address: Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,

  2. Pau Creixell and Jüri Reimand: These authors contributed equally to this work.

Authors and Affiliations

  1. Cellular Signal Integration Group (C-SIG), Technical University of Denmark, Lyngby, Denmark

    Pau Creixell & Rune Linding

  2. The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada

    Jüri Reimand & Gary D Bader

  3. Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada

    Syed Haider, Guanming Wu, B F Francis Ouellette, Paul C Boutros & Lincoln D Stein

  4. Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon, USA

    Guanming Wu

  5. Division of Cancer Genomics, National Cancer Center, Tokyo, Japan

    Tatsuhiro Shibata

  6. Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain

    Miguel Vazquez & Alfonso Valencia

  7. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,

    Ville Mustonen

  8. Research Unit on Biomedical Informatics, University Pompeu Fabra, Barcelona, Spain

    Abel Gonzalez-Perez & Nuria Lopez-Bigas

  9. Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, Queensland, Australia

    John Pearson

  10. Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, USA

    Chris Sander

  11. Department of Computer Science and Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, USA

    Benjamin J Raphael

  12. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA

    Debora S Marks

  13. Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada

    B F Francis Ouellette

  14. Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada

    Paul C Boutros

  15. Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada

    Paul C Boutros

  16. Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, USA.,

    Joshua M Stuart

  17. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California, USA.,

    Joshua M Stuart

  18. Biotech Research & Innovation Centre (BRIC), University of Copenhagen (UCPH), Copenhagen, Denmark

    Rune Linding

  19. Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain

    Nuria Lopez-Bigas

  20. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada

    Lincoln D Stein

Consortia

the Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium

  • Pau Creixell
  • , Jüri Reimand
  • , Syed Haider
  • , Guanming Wu
  • , Tatsuhiro Shibata
  • , Miguel Vazquez
  • , Ville Mustonen
  • , Abel Gonzalez-Perez
  • , John Pearson
  • , Chris Sander
  • , Benjamin J Raphael
  • , Debora S Marks
  • , B F Francis Ouellette
  • , Alfonso Valencia
  • , Gary D Bader
  • , Paul C Boutros
  • , Joshua M Stuart
  • , Rune Linding
  • , Nuria Lopez-Bigas
  •  & Lincoln D Stein

Corresponding author

Correspondence to Lincoln D Stein.

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The author declare no competing financial interests.

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the Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium. Pathway and network analysis of cancer genomes. Nat Methods 12, 615–621 (2015). https://doi.org/10.1038/nmeth.3440

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