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Sample-specific perturbation of gene interactions identifies breast cancer subtypes

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...

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Detalles Bibliográficos
Autores principales: Chen, Yuanyuan, Gu, Yu, Hu, Zixi, Sun, Xiao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8293822/
https://www.ncbi.nlm.nih.gov/pubmed/33126248
http://dx.doi.org/10.1093/bib/bbaa268
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author Chen, Yuanyuan
Gu, Yu
Hu, Zixi
Sun, Xiao
author_facet Chen, Yuanyuan
Gu, Yu
Hu, Zixi
Sun, Xiao
author_sort Chen, Yuanyuan
collection PubMed
description 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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spelling pubmed-82938222021-07-22 Sample-specific perturbation of gene interactions identifies breast cancer subtypes Chen, Yuanyuan Gu, Yu Hu, Zixi Sun, Xiao Brief Bioinform Problem Solving Protocol 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. Oxford University Press 2020-10-30 /pmc/articles/PMC8293822/ /pubmed/33126248 http://dx.doi.org/10.1093/bib/bbaa268 Text en © The Author(s) 2020. Published by Oxford University Press. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Problem Solving Protocol
Chen, Yuanyuan
Gu, Yu
Hu, Zixi
Sun, Xiao
Sample-specific perturbation of gene interactions identifies breast cancer subtypes
title Sample-specific perturbation of gene interactions identifies breast cancer subtypes
title_full Sample-specific perturbation of gene interactions identifies breast cancer subtypes
title_fullStr Sample-specific perturbation of gene interactions identifies breast cancer subtypes
title_full_unstemmed Sample-specific perturbation of gene interactions identifies breast cancer subtypes
title_short Sample-specific perturbation of gene interactions identifies breast cancer subtypes
title_sort sample-specific perturbation of gene interactions identifies breast cancer subtypes
topic Problem Solving Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8293822/
https://www.ncbi.nlm.nih.gov/pubmed/33126248
http://dx.doi.org/10.1093/bib/bbaa268
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