How to find cell-specific enhancer-promoter interactions?
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5.2 years ago
Sama ▴ 60

I extracted enhancer-promoter interactions of Gm12878, HMEC cells from Hi-C data and I want to have the cell specific interactions of each cell line. I assumed, when in two interactions their promoters are overlapping and their enhancers are overlapping as well, I considered them to be the same. Using this assumption, I extracted shared interactions of cells to consider them as conserved interactions so the rest of interactions in each cell would be cell specific. However, the problem is that using this method, only 20 conserved interactions were found which I know is very low and I know there are many shared interactions between each two cells. I could not find how others extract cell specific interactions. Can anybody help me?

gene regulation cell specific interactions • 1.4k views

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