biostudies-literatureUnknown41(8)Mullen DJUSC Center for Genetic EpidemiologyJohn H. Richardson Endowed Postdoctoral Fellowship in Oncology ResearchUSC Keck School of MedicineUSC Norris Comprehensive Cancer Center<h4>Summary</h4>There is a lack of publicly available bioinformatic tools that can be widely used by researchers to identify transcription factors (TFs) that regulate cell type-specific regulatory elements (REs). To address this, we developed the Tracing regulatory Element Networks using Epigenetic Traits (TENET) R/Bioconductor package. By collecting hundreds of histone mark and open chromatin datasets from a variety of cell lines, primary cells, and tissues, and comparing these features along with matched DNA methylation and gene expression data, TENET identifies TFs and REs linked to a specific cell type. Moreover, we developed methods to interrogate findings using motifs, clinical information, and other genomic and chromatin conformation capture datasets, and applied them to pan-cancer data, highlighting TFs and REs associated with ten different cancer types. TENET enables researchers to better characterize the 3D epigenomes of cell types of interest for future clinical applications.<h4>Availability and implementation</h4>TENET is available at http://bioconductor.org/packages/TENET. Curated functional genomic datasets utilized by TENET are available at http://bioconductor.org/packages/TENET.AnnotationHub. Example datasets are available at http://bioconductor.org/packages/TENET.ExperimentHub.Bioinformatics (Oxford, England)btaf435https://www.ebi.ac.uk/biostudies/studies/S-EPMC12349384biostudies-literatureTracing regulatory element networks using epigenetic traits to identify key transcription factors: TENET R/Bioconductor package.PMC12349384Wu ZCao HHan LNelson-Moore EMullen DJRhie SKOffringa IAfalseTracing regulatory element networks using epigenetic traits to identify key transcription factors: TENET R/Bioconductor package.<h4>Summary</h4>There is a lack of publicly available bioinformatic tools that can be widely used by researchers to identify transcription factors (TFs) that regulate cell type-specific regulatory elements (REs). To address this, we developed the Tracing regulatory Element Networks using Epigenetic Traits (TENET) R/Bioconductor package. By collecting hundreds of histone mark and open chromatin datasets from a variety of cell lines, primary cells, and tissues, and comparing these features along with matched DNA methylation and gene expression data, TENET identifies TFs and REs linked to a specific cell type. Moreover, we developed methods to interrogate findings using motifs, clinical information, and other genomic and chromatin conformation capture datasets, and applied them to pan-cancer data, highlighting TFs and REs associated with ten different cancer types. TENET enables researchers to better characterize the 3D epigenomes of cell types of interest for future clinical applications.<h4>Availability and implementation</h4>TENET is available at http://bioconductor.org/packages/TENET. Curated functional genomic datasets utilized by TENET are available at http://bioconductor.org/packages/TENET.AnnotationHub. Example datasets are available at http://bioconductor.org/packages/TENET.ExperimentHub.2025-01-01T00:00:00Z2025 Aug2026-04-30T15:46:57.594Z2026-04-07T16:09:12.842ZS-EPMC123493844074871210.1093/bioinformatics/btaf435