DHC-MEGE

What does it do?
DHC-MEGE is a program designed for the identification of functional long-range cis elements such as enhancers from gene expression data.

How does it work?
DHC-MEGE takes a list of up- and down-regulated genes and extracts regions from a chromatin connectivity map which are predicted to physically associate with those genes. It then searches for over-represented sequence motifs and then reports instances of those motifs throughout the genome.

What is the input?
You need a list of up genes, down genes, a DNase hypersensitivity connectivity map (BED8 format) and genome sequence (fasta format).

What is the output?
The main output is the GMT file, which is a list of gene lists which details the occurance of sequence motifs across the hypersensitive regions of the genome.

How can I use the output file?
GMT files can be used in gene set enrichment analysis of the array/mRNA-seq experiment.

More info in the manual.