De Novo Pathway-Based Classification of Breast Cancer Subtypes

Markus List; Nicolas Alcaraz; Richa Batra

doi:10.1007/978-1-4939-9873-9_15

De Novo Pathway-Based Classification of Breast Cancer Subtypes

Markus List^*, Nicolas Alcaraz, Richa Batra

^*Corresponding author af dette arbejde

Bioinformatik og RNA Biologi

1 Citationer (Scopus)

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/.

Originalsprog	Engelsk
Titel	Protein-Protein Interaction Networks : Methods and Protocols
Redaktører	Stefan Canzar, Francisca Rojas Ringeling
Antal sider	13
Forlag	Humana Press
Publikationsdato	2020
Sider	201-213
Kapitel	15
ISBN (Trykt)	978-1-4939-9872-2
ISBN (Elektronisk)	978-1-4939-9873-9
DOI	https://doi.org/10.1007/978-1-4939-9873-9_15
Status	Udgivet - 2020

Navn	Methods in Molecular Biology
Vol/bind	2074
ISSN	1064-3745

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10.1007/978-1-4939-9873-9_15

Citationsformater

De Novo Pathway-Based Classification of Breast Cancer Subtypes. / List, Markus; Alcaraz, Nicolas; Batra, Richa.

Protein-Protein Interaction Networks: Methods and Protocols. red. / Stefan Canzar; Francisca Rojas Ringeling. Humana Press, 2020. s. 201-213 (Methods in Molecular Biology, Bind 2074).

Publikation: Bidrag til bog/antologi/rapport › Bidrag til bog/antologi › Forskning › peer review

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AB - 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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KW - De novo pathways

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De Novo Pathway-Based Classification of Breast Cancer Subtypes

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