ArticleBioinformatics (Oxford, England)2020
Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 8 citations in OpenAlex.
- Aberrant Transcription-Factor Expression and Regulatory microRNAs in Metastatic Breast Cancer.Cells · 2026Review
- Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages.Nature cancer · 2024Article
- The crosstalk role of CDKN2A between tumor progression and cuproptosis resistance in colorectal cancer.Aging · 2024Article
- INO80 function is required for mouse mammary gland development, but mutation alone may be insufficient for breast cancer.Frontiers in cell and developmental biology · 2023Article
- Chromatin Variants Reveal the Genetic Determinants of Oncogenesis in Breast Cancer.Cold Spring Harbor perspectives in medicine · 2022Review
- Subtype and cell type specific expression of lncRNAs provide insight into breast cancer.Communications biology · 2022Article
Corrections and comments
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Authors and funding
4 authors at 4 institutions in 2 countries.
Funding
Abstract
motivationBreast cancer consists of multiple distinct tumor subtypes, and results from epigenetic and genetic aberrations that give rise to distinct transcriptional profiles. Despite previous efforts to understand transcriptional deregulation through transcription factor networks, the transcriptional mechanisms leading to subtypes of the disease remain poorly understood.
resultsWe used a sophisticated computational search of thousands of expression datasets to define extended signatures of distinct breast cancer subtypes. Using ENCODE ChIP-seq data of surrogate cell lines and motif analysis we observed that these subtypes are determined by a distinct repertoire of lineage-specific transcription factors. Furthermore, specific pattern and abundance of copy number and DNA methylation changes at these TFs and targets, compared to other genes and to normal cells were observed. Overall, distinct transcriptional profiles are linked to genetic and epigenetic alterations at lineage-specific transcriptional regulators in breast cancer subtypes. AVAILABILITY AND IMPLEMENTATION: The analysis code and data are deposited at https://bitbucket.org/qzhu/breast.cancer.tf/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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