Software

TENET: Tracing Enhancer Networks using Epigenetic Traits

 

TENET program dependencies

1. bedtools (please install from https://github.com/arq5x/bedtools2/releases)

2. bioconductor R packages, ELMER, parallel, ggplot2, and RCircos (can be installed using bioconductor by typing below in R)

    source("http://bioconductor.org/biocLite.R")

    biocLite("ELMER")

    biocLite("parallel")

    biocLite("ggplot2")

    biocLite("RCircos")

 

TENET installation

- Download the TENET program here and unzip by typing below 

    tar -xvzf TENET.tar.gz

- Put DNA methylation and gene expression data with matched sample IDs

- fill out parameter settings in settings.txt

- run TENET by typing below

    bash ./TENET.sh

 

Please read the detailed instruction manual

Example datasets for TENET

 

Citation 

Rhie SK et al. Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits. Epigenetics Chromatin 2016 Nov 9;9:50. PMID: 27833659