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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.<\/jats:p>","DOI":"10.1093\/bib\/bbaa268","type":"journal-article","created":{"date-parts":[[2020,9,18]],"date-time":"2020-09-18T11:23:27Z","timestamp":1600428207000},"source":"Crossref","is-referenced-by-count":37,"title":["Sample-specific perturbation of gene interactions identifies breast cancer subtypes"],"prefix":"10.1093","volume":"22","author":[{"given":"Yuanyuan","family":"Chen","sequence":"first","affiliation":[{"name":"College of Science, Nanjing Agricultural University, Jiangsu, Nanjing, China, and a postdoc at State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Gu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zixi","family":"Hu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao","family":"Sun","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,10,30]]},"reference":[{"key":"2021072112311722100_ref1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pmed.1000279","article-title":"Subtyping of breast cancer by immunohistochemistry to investigate a relationship between subtype and short and long term survival: a collaborative analysis of data for 10,159 cases 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