chromgenie
A tool to correlate gene expression changes with epigenetic changes
... with HUGO gene symbol in the first column and fold change (typically log base 2) in the second column.
2. A bed file of genomic sites showing dynamic signal between the two conditions used for gene expression testing, with fold change in signal in the 4th column.
3. A bed file of the genomic coordinate of genes with a HUGO gene symbol in the 4th column. Dynamic sites from file 2 are then annotated to the nearest gene. Potentially using TSS instead of whole gene body can help.