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De Novo Pathway-Based Classification of Breast Cancer Subtypes

  • Markus ListEmail author
  • Nicolas Alcaraz
  • Richa Batra
Protocol
Part of the Methods in Molecular Biology book series (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/.

Key words

De novo pathways Disease subtyping Breast cancer Classification 

Notes

Acknowledgments

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

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.TUM School of Life SciencesTechnical University of MunichFreisingGermany
  2. 2.Department of Biology, The Bioinformatics CentreUniversity of CopenhagenCopenhagenDenmark
  3. 3.Helmholtz Zentrum München, Research Center for Environmental HealthInstitute of Computational BiologyNeuherbergGermany
  4. 4.Department of Dermatology and AllergyTechnical University of MunichMünchenGermany

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