ArticleFrontiers in genetics2019
Master Regulators of Signaling Pathways: An Application to the Analysis of Gene Regulation in Breast Cancer.
Article in Frontiers in genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- A β-Hydroxybutyrylation-FOXM1/CENPA Axis Links Ketone-Body Metabolism to Mitotic Transcription in Basal-like Breast Cancer.International journal of molecular sciences · 2026Article
- CTAS: a network control theory-based approach to identify key regulatory TFs of AS events during epithelial-mesenchymal transition.Briefings in bioinformatics · 2026Article
- System analysis links SMARCD3 regulons to growth signaling and MEK inhibitor response in everolimus-resistant ER+ breast cancer cells.Cell reports. Medicine · 2025Article
- Diverse oncogenes use common mechanisms to drive growth of major forms of human cancer.Science advances · 2025Article
- Coordinated inflammation and immune response transcriptional regulation in breast cancer molecular subtypes.Frontiers in immunology · 2024Article
- Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontia.BMC oral health · 2023Article
- Molecular mechanisms of multi-omic regulation in breast cancer.Frontiers in oncology · 2023Review
- The regulatory landscape of retinoblastoma: a pathway analysis perspective.Royal Society open science · 2022Article
- The genomic landscape of pediatric renal cell carcinomas.iScience · 2022Article
- Functional impact of multi-omic interactions in breast cancer subtypes.Frontiers in genetics · 2022Article
- Early-life social experience affects offspring DNA methylation and later life stress phenotype.Nature communications · 2021Article
- A functional outside-in signaling network of proteoglycans and matrix molecules regulating autophagy.Matrix biology : journal of the International Society for Matrix Biology · 2021Article
- MZ1 co-operates with trastuzumab in HER2 positive breast cancer.Journal of experimental & clinical cancer research : CR · 2021Article
- Dysregulation of Transcription Factor Networks Unveils Different Pathways in Human Papillomavirus 16-Positive Squamous Cell Carcinoma and Adenocarcinoma of the Uterine Cervix.Frontiers in oncology · 2021Article
- Gene Co-Expression in Breast Cancer: A Matter of Distance.Frontiers in oncology · 2021Article
- Transcriptional Regulation of Cancer Immune Checkpoints: Emerging Strategies for Immunotherapy.Vaccines · 2020Review
- miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems.Nucleic acids research · 2020Article
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4 authors.
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Abstract
Analysis of gene regulatory networks allows the identification of master transcriptional factors that control specific groups of genes. In this work, we inferred a gene regulatory network from a large dataset of breast cancer samples to identify the master transcriptional factors that control the genes within signal transduction pathways. The focus in a particular subset of relevant genes constitutes an extension of the original Master Regulator Inference Algorithm (MARINa) analysis. This modified version of MARINa utilizes a restricted molecular signature containing genes from the 25 human pathways in KEGG's signal transduction category. Our breast cancer RNAseq expression dataset consists of 881 samples comprising tumors and normal mammary gland tissue. The top 10 master transcriptional factors found to regulate signal transduction pathways in breast cancer we identified are: TSHZ2, HOXA2, MEIS2, HOXA3, HAND2, HOXA5, TBX18, PEG3, GLI2, and CLOCK. The functional enrichment of the regulons of these master transcriptional factors showed an important proportion of processes related to morphogenesis. Our results suggest that, as part of the aberrant regulation of signaling pathways in breast cancer, pathways similar to the regulation of cell differentiation, cardiovascular system development, and vasculature development may be dysregulated and co-opted in favor of tumor development through the action of these transcription factors.
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