Sample-specific Perturbation of Gene Interactions Identifies Breast Cancer Subtypes

Overview

Journal Brief Bioinform

Publisher Oxford University Press

Specialty Biology

Date 2020 Oct 30

PMID 33126248

Citations 14

Authors

Yuanyuan Chen

Yu Gu

Zixi Hu

Xiao Sun

Affiliations

Soon will be listed here.

Abstract

Breast cancer is a highly heterogeneous disease, and there are many forms of categorization for breast cancer based on gene expression profiles. Gene expression profiles are variables and may show differences if measured at different time points or under different conditions. In contrast, biological networks are relatively stable over time and under different conditions. In this study, we used a gene interaction network from a new point of view to explore the subtypes of breast cancer based on individual-specific edge perturbations measured by relative gene expression value. Our study reveals that there are four breast cancer subtypes based on gene interaction perturbations at the individual level. The new network-based subtypes of breast cancer show strong heterogeneity in prognosis, somatic mutations, phenotypic changes and enriched pathways. The network-based subtypes are closely related to the PAM50 subtypes and immunohistochemistry index. This work helps us to better understand the heterogeneity and mechanisms of breast cancer from a network perspective.

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