De Novo Pathway-Based Classification of Breast Cancer Subtypes

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  • Markus List
  • Nicolas Alcaraz
  • Richa Batra

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/.

Original languageEnglish
Title of host publicationProtein-Protein Interaction Networks : Methods and Protocols
EditorsStefan Canzar, Francisca Rojas Ringeling
Number of pages13
PublisherHumana Press
Publication date2020
Pages201-213
Chapter15
ISBN (Print)978-1-4939-9872-2
ISBN (Electronic)978-1-4939-9873-9
DOIs
Publication statusPublished - 2020
SeriesMethods in Molecular Biology
Volume2074
ISSN1064-3745

    Research areas

  • Breast cancer, Classification, De novo pathways, Disease subtyping

ID: 230742706