Identification of Molecular Subtypes in Pancreatic Adenocarcinoma with Predictive and Prognostic Importance

doi:10.1038/protex.2011.231

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Method Article

Joe Gray, Anguraj Sadanandam, Eric Collisson, William Gibb, Douglas Hanahan

Joe Gray

Oregon Health and Science University

Corresponding Author

Anguraj Sadanandam

Ecole Polytechnique Federale de Lausanne

Eric Collisson

University of California at San Francisco

William Gibb

Genomic Health

Douglas Hanahan

Ecole Polytechnique Federale de Lausanne

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In this protocol, we describe methodologies used in the Nature Medicine manuscript “Subtypes of Pancreatic Ductal Adenocarcinoma and their Differing Response to Therapy”. Herein, we describe the computational pipeline used to identify subtypes of pancreatic ductal adenocarcinoma and their associated gene signature using integrated analysis of various gene expression profiles with clinical outcome.

Keywords

cancer subtypes, pancreatic cancer, NMF, DWD

William Gibb is an employee of Genomic Health.

This is a list of supplementary files associated with this preprint. Click to download.

supplement0.r
ScreenExpression.r To screen variable and unique genes This R code can be used to screen for those genes with standard deviation greater than certain cutoff. In addition, in cases where multiple probes are available for a single gene, it selects only one probe with highest standard deviation for that gene.

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Associated Publications

Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy
by Eric A Collisson, Anguraj Sadanandam, Peter Olson, +13
Nature Medicine (17 March, 2011)

An open repository of community-contributed protocols sponsored by Nature Research.

Learn more about Protocol Exchange

Method Article

Joe Gray, Anguraj Sadanandam, Eric Collisson, William Gibb, Douglas Hanahan

Joe Gray

Oregon Health and Science University

Corresponding Author

Anguraj Sadanandam

Ecole Polytechnique Federale de Lausanne

Eric Collisson

University of California at San Francisco

William Gibb

Genomic Health

Douglas Hanahan

Ecole Polytechnique Federale de Lausanne

Version History

CURRENT STATUS: Posted

Version 1

Posted 04 Apr, 2011

No community comments so far

MetricsComments: 0HTML Views: ...

Subject Areas

Computational biology and bioinformatics

Biotechnology

DOI:

10.1038/protex.2011.231

Download PDF

The full text of this article is available to read as a PDF.

License:

This work is licensed under a CC BY-NC 3.0 License. Read Full License

William Gibb is an employee of Genomic Health.

This is a list of supplementary files associated with this preprint. Click to download.

supplement0.r
ScreenExpression.r To screen variable and unique genes This R code can be used to screen for those genes with standard deviation greater than certain cutoff. In addition, in cases where multiple probes are available for a single gene, it selects only one probe with highest standard deviation for that gene.

Associated Publications

Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy
by Eric A Collisson, Anguraj Sadanandam, Peter Olson, +13
Nature Medicine (17 March, 2011)

An open repository of community-contributed protocols sponsored by Nature Research.

Learn more about Protocol Exchange

Method Article

Joe Gray, Anguraj Sadanandam, Eric Collisson, William Gibb, Douglas Hanahan

Joe Gray

Oregon Health and Science University

Corresponding Author

Anguraj Sadanandam

Ecole Polytechnique Federale de Lausanne

Eric Collisson

University of California at San Francisco

William Gibb

Genomic Health

Douglas Hanahan

Ecole Polytechnique Federale de Lausanne

DOI:

10.1038/protex.2011.231

Download PDF

License:

This work is licensed under a CC BY-NC 3.0 License. Read Full License

Abstract

Keywords

cancer subtypes, pancreatic cancer, NMF, DWD

Introduction

Procedure

References

Competing Interests

Supplementary Files

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Version History

CURRENT STATUS: Posted

Version 1

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Subject Areas

Computational biology and bioinformatics

Biotechnology

Associated Publications

Subtypes of pancreatic ductal adenocarcinoma and their differing responses to therapy

by Eric A Collisson, Anguraj Sadanandam, Peter Olson, +13

Nature Medicine (17 March, 2011)

An open repository of community-contributed protocols sponsored by Nature Research.

Learn more about Protocol Exchange

Method Article

Joe Gray, Anguraj Sadanandam, Eric Collisson, William Gibb, Douglas Hanahan

Joe Gray

Oregon Health and Science University

Corresponding Author

Anguraj Sadanandam

Ecole Polytechnique Federale de Lausanne

Eric Collisson

University of California at San Francisco

William Gibb

Genomic Health

Douglas Hanahan

Ecole Polytechnique Federale de Lausanne

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CURRENT STATUS: Posted

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Subject Areas

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DOI & PDF

DOI:

10.1038/protex.2011.231

Download PDF

License

License:

This work is licensed under a CC BY-NC 3.0 License. Read Full License

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