3.5 years ago by
Are you trying to find enhancers in a specific cell type ? You can get enhancer data from fantom database of other cell types ( say blood cells for comparison with liver tissue ) to increase specificity of the classifier in your cell type.
Alternatively a gross estimate of negative regions could be take all enhancer regions from ENCODE ( incase you dont want any regulatory regions - extend this to regions for marks - H3k4me3, me1 and 27ac ) across all cell types and get a list of regions that dont overlap any of these.
I would be more comfortable with a tissue specific approach because the presence or absence of a histone mark and "thus a regulatory region" is too broad and dependant on the protocol, tissue, thresholds etc.