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De Novo Pathway-Based Classification of Breast Cancer Subtypes

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Protein-Protein Interaction Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2074))

Abstract

Breast cancer is a heterogeneous disease for which various clinically relevant subtypes have been reported. These subtypes are characterized by molecular differences which direct treatment selection. The state of the art for breast cancer subtyping utilizes histochemistry or gene expression to measure a few selected markers. However, classification based on molecular pathways (rather than individual markers) is a more robust way to classify breast cancer samples into known subtypes.

Here, we present PathClass, a web application that allows its users to predict breast cancer subtypes using various traditional as well as advanced methods. This includes methods based on classical gene expression panels as well as de novo pathway-based predictors. Users can predict labels for datasets in the Gene Expression Omnibus or upload their own expression profiling data.

Availability: https://pathclass.compbio.sdu.dk/.

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Acknowledgments

R.B. would like to thank 676858-IMCIS for funding.

Author information

Authors and Affiliations

  1. TUM School of Life Sciences, Technical University of Munich, Freising, Germany

    Markus List

  2. Department of Biology, The Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark

    Nicolas Alcaraz

  3. Helmholtz Zentrum München, Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany

    Richa Batra

  4. Department of Dermatology and Allergy, Technical University of Munich, München, Germany

    Richa Batra

Authors
  1. Markus List
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  2. Nicolas Alcaraz
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  3. Richa Batra
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Corresponding author

Correspondence to Markus List .

Editor information

Editors and Affiliations

  1. Gene Center, Ludwig-Maximilians-Universität München, München, Germany

    Stefan Canzar

  2. Gene Center, Ludwig-Maximilians-Universität München, München, Germany

    Francisca Rojas Ringeling

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List, M., Alcaraz, N., Batra, R. (2020). De Novo Pathway-Based Classification of Breast Cancer Subtypes. In: Canzar, S., Ringeling, F. (eds) Protein-Protein Interaction Networks. Methods in Molecular Biology, vol 2074. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9873-9_15

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  • DOI: https://doi.org/10.1007/978-1-4939-9873-9_15

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9872-2

  • Online ISBN: 978-1-4939-9873-9

  • eBook Packages: Springer Protocols

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