Tracing regulatory element networks using epigenetic traits to identify key transcription factors: TENET R/Bioconductor package.

Abstract

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. 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.