{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["41(8)"],"submitter":["Mullen DJ"],"funding":["USC Center for Genetic Epidemiology","John H. Richardson Endowed Postdoctoral Fellowship in Oncology Research","USC Keck School of Medicine","USC Norris Comprehensive Cancer Center"],"pubmed_abstract":["<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."],"journal":["Bioinformatics (Oxford, England)"],"pagination":["btaf435"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC12349384"],"repository":["biostudies-literature"],"pubmed_title":["Tracing regulatory element networks using epigenetic traits to identify key transcription factors: TENET R/Bioconductor package."],"pmcid":["PMC12349384"],"pubmed_authors":["Wu Z","Cao H","Han L","Nelson-Moore E","Mullen DJ","Rhie SK","Offringa IA"],"additional_accession":[]},"is_claimable":false,"name":"Tracing regulatory element networks using epigenetic traits to identify key transcription factors: TENET R/Bioconductor package.","description":"<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.","dates":{"release":"2025-01-01T00:00:00Z","publication":"2025 Aug","modification":"2026-04-30T15:46:57.594Z","creation":"2026-04-07T16:09:12.842Z"},"accession":"S-EPMC12349384","cross_references":{"pubmed":["40748712"],"doi":["10.1093/bioinformatics/btaf435"]}}