Network-based approach elucidates critical genes in BRCA subtypes and chemotherapy response in triple negative breast cancer.

ABSTRACT: Breast cancers (BRCA) exhibit substantial transcriptional heterogeneity, posing a significant clinical challenge. The global transcriptional changes in a disease context, however, are likely mediated by few key genes which reflect disease etiology better than the differentially expressed genes (DEGs). We apply our network-based tool PathExt to 1,059 BRCA tumors across 4 subtypes to identify key mediator genes in each subtype. Compared to conventional differential expression analysis, PathExt-identified genes exhibit greater concordance across tumors, revealing shared and subtype-specific biological processes; better recapitulate BRCA-associated genes in multiple benchmarks, and are more essential in BRCA subtype-specific cell lines. Single-cell transcriptomic analysis reveals a subtype-spe

SUBMITTER: Agrawal P 

PROVIDER: S-EPMC11063905 | biostudies-literature | 2024 May

REPOSITORIES: biostudies-literature