I am working on regulation of gene expression of a gene and i want to check the status of it enhancer in cancer cells.
can you suggest software to use ,and what are the important things to take in consideration while looking for gene enhancer ?
thank you.
Hello,
There is ENCODE (https://www.encodeproject.org/) for regulatory elements. It is also accessible via UCSC genome browser (just select show for ENCODE regulatory elements part). By a quick search I have found another tool just for enhancers, VISTA Enhancer Browser (http://enhancer.lbl.gov/). I have never used it but it says they only have experimentally proven data, so I suggest you to give it a try.
FANTOM consortia published data-sets on active enhancers
An atlas of active enhancers across human cell types and tissues
http://www.nature.com/nature/journal/v507/n7493/abs/nature12787.html
Could you elaborate on the type of data your have and what you mean by 'looking for the enhancer'? What 'cancer cells' are you using? If it's a cell line, has it been profiled by ENCODE? Do you already know where the enhancer is and are trying to see if it's active? Or are you trying to find the enhancer(s) for this gene? Both ENCODE and FANTOM are excellent resources, but they are merely genome wide annotations of chromatin states and enhancers respectively. They are not going to tell you which enhancers regulate your gene .You could potentially use them to find nearest enhancers to your gene. But enhancers could be many kb away from their target gene. You might need to rely on chromatin capture data for that.
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