chromgenie

Changes in cellular gene expression may occur in response to stimuli or development. There may be simultaneous changes in histone marks and transcription factor binding. How these relate to gene expression changes is often unclear.
This tool was written to detect correlations between changes in gene expression between two conditions and concurrent changes in histone marks or transcription factor binding events.
The user supplies three files.
1. A tab delimited file of gene expression 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.