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Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations

Author(s): Zhu, Qian; Tekpli, Xavier; Troyanskaya, Olga G; Kristensen, Vessela N

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Abstract: Motivation Breast 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. Results We 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.
Publication Date: 15-Feb-2020
Citation: Zhu, Qian, Xavier Tekpli, Olga G. Troyanskaya, and Vessela N. Kristensen. "Subtype-specific transcriptional regulators in breast tumors subjected to genetic and epigenetic alterations." Bioinformatics 36, no. 4 (2020): 994-999. doi:10.1093/bioinformatics/btz709
DOI: 10.1093/bioinformatics/btz709
ISSN: 1367-4803
EISSN: 1460-2059
Pages: 994 - 999
Language: eng
Type of Material: Journal Article
Journal/Proceeding Title: Bioinformatics
Version: Final published version. This is an open access article.
Notes: Links to code, data, and supplementary information at

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