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Guided visual exploration of genomic stratifications in cancer

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Figure 1: Seamless integration of visual and computational components in the extended StratomeX tool.

References

  1. Verhaak, R. et al. Cancer Cell 17, 98–110 (2010).

    Article  CAS  Google Scholar 

  2. Hofree, M., Shen, J. P., Carter, H., Gross, A. & Ideker, T. Nat. Methods 10, 1108–1115 (2013).

    Article  CAS  Google Scholar 

  3. Lex, A. et al. Computer Graphics Forum 31, 1175–1184 (2012).

    Article  CAS  Google Scholar 

  4. Schroeder, M.P., Gonzalez-Perez, A. & Lopez-Bigas, N. Genome Med. 5, 9 (2013)

    Article  Google Scholar 

  5. Gratzl, S., Lex, A., Gehlenborg, N., Pfister, H.P. & Streit, M. IEEE Trans. Visualization Computer Graphics 19, 2277–2286 (2013).

    Article  Google Scholar 

  6. The Cancer Genome Atlas Research Network. Nature 499, 43–49 (2013).

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Acknowledgements

This work was supported by US National Institutes of Health (U24 CA144025, U24 CA143845 and K99 HG007583), the Austrian Science Fund (J 3437-N15, P 22902), and the Air Force Research Laboratory and Defense Advanced Research Projects Agency grant FA8750-12-C-0300.

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Author notes

  1. Marc Streit and Alexander Lex: These authors contributed equally to this work.

Authors and Affiliations

  1. Institute of Computer Graphics, Johannes Kepler University Linz, Linz, Austria

    Marc Streit & Samuel Gratzl

  2. School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA

    Alexander Lex & Hanspeter Pfister

  3. Institute for Computer Graphics and Vision, Graz University of Technology, Graz, Austria

    Christian Partl & Dieter Schmalstieg

  4. Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA

    Peter J Park & Nils Gehlenborg

  5. Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA

    Nils Gehlenborg

Authors
  1. Marc Streit
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  2. Alexander Lex
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  3. Samuel Gratzl
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  4. Christian Partl
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  5. Dieter Schmalstieg
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  6. Hanspeter Pfister
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  7. Peter J Park
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  8. Nils Gehlenborg
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Corresponding authors

Correspondence to Peter J Park or Nils Gehlenborg.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–18, Supplementary Tables 1–3, Supplementary Discussion, Supplementary Note and Supplementary Methods (PDF 10088 kb)

Supplementary Data 1

The Cancer Genome Atlas clear cell renal carcinoma dataset for Caleydo including microRNA- and mRNA-based patient subtype assignments reported in the TCGA consortium paper. (ZIP 72700 kb)

Supplementary Data 2

List of significantly mutated genes and their q-values generated by the Firehose MutSig v2.0 module. (TXT 1941 kb)

Supplementary Data 3

Tumor suppressor gene and oncogene classification. (TXT 1 kb)

Supplementary Data 4

Silent and nonsilent mutation rates for all available clear cell renal carcinoma patient genomes available in The Cancer Genomce Atlas project from the MutSig 2.0 Firehose pipeline run of 23 May 2013. (TXT 24 kb)

Supplementary Video 1

Video demonstrating the StratomeX user interface, visualizations and query wizard. (MP4 59908 kb)

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Streit, M., Lex, A., Gratzl, S. et al. Guided visual exploration of genomic stratifications in cancer. Nat Methods 11, 884–885 (2014). https://doi.org/10.1038/nmeth.3088

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  • DOI: https://doi.org/10.1038/nmeth.3088

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