ArticleGenome biology2017
Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network.
Article in Genome biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Leveraging sequences missing from the human genome to diagnose cancer.Communications medicine · 2025Article
- Discovery of therapeutic targets in cancer using chromatin accessibility and transcriptomic data.Cell systems · 2024Article
- The Regulatory Network of CREB3L1 and Its Roles in Physiological and Pathological Conditions.International journal of medical sciences · 2024Review
- The endoplasmic reticulum stress response in prostate cancer.Nature reviews. Urology · 2022Review
- Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets.Science (New York, N.Y.) · 2022Article
- Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure.BMC genomic data · 2022Article
- The most effective but largely ignored target for prostate cancer early detection and intervention.Journal of Cancer · 2022Article
- Article
- Mechanism-Centric Approaches for Biomarker Detection and Precision Therapeutics in Cancer.Frontiers in genetics · 2021Review
- Integrative computational epigenomics to build data-driven gene regulation hypotheses.GigaScience · 2020Article
- Complex impact of DNA methylation on transcriptional dysregulation across 22 human cancer types.Nucleic acids research · 2020Article
- MutSpot: detection of non-coding mutation hotspots in cancer genomes.NPJ genomic medicine · 2020Article
- ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles.Bioinformatics (Oxford, England) · 2019Article
- Emerging Roles of the Endoplasmic Reticulum Associated Unfolded Protein Response in Cancer Cell Migration and Invasion.Cancers · 2019Review
- BayesPI-BAR2: A New Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts.Frontiers in genetics · 2019Article
- Integrative (epi) Genomic Analysis to Predict Response to Androgen-Deprivation Therapy in Prostate Cancer.EBioMedicine · 2018Article
- ERF deletion rescues RAS deficiency in mouse embryonic stem cells.Genes & development · 2018Article
- Statistical and integrative system-level analysis of DNA methylation data.Nature reviews. Genetics · 2018Review
- Systems-epigenomics inference of transcription factor activity implicates aryl-hydrocarbon-receptor inactivation as a key event in lung cancer development.Genome biology · 2017Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation changes in the DNase I hypersensitivity based regulatory network. Integration of multi-omics data from 521 prostate tumor samples indicated a stronger regulatory impact of structural variants, as they affect more transcription factor hubs in the tissue-specific network. Moreover, crosstalk between transcription factor hub expression modulated by structural variants and methylation levels likely leads to the differential expression of target genes. We report known prostate tumor regulatory drivers and nominate novel transcription factors (ERF, CREB3L1, and POU2F2), which are supported by functional validation.
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