Hi,
I've a bunch of genomic positions and I want to check if these positions are enriched in TF binding sites or enchancer ? My idea was to use ENCODE data and to do a simulation like this :
What do you think ? Other ideas ?
Thanks
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Nicolas Rosewick
This is how I'd approach the problem as well. One thing to keep in mind is that enhancers and promoters can be cell-type specific. In an ideal world, you'd just want to look in your cell-type of interest. Also, do make sure that regions have evolutionary conservation (i.e., try not to make the same mistakes as ENCODE). A final thing to think about is whether it makes sense to look at TF binding site in toto or whether it makes sense to just look at individual transcription factors. I say this since the meaningfulness of the results there's a slight enrichment due to complete enrichment of one or two TF binding motifs vs. a generic mild enrichment of everything (i.e., a slight but significant global enrichment is likely due simply to an uncompensated bias).
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Devon Ryan
Thanks Devon. Yes of course I'll take the right cell type. When you say areas with similar mappability, what do you mean?
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Nicolas Rosewick
Just that you don't want to randomly draw from an area with a bunch of N's or that the TF binding sites would never have been called in to begin with (these would likely include repeat regions, though perhaps not).
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Devon Ryan
ok thanks that's a good idea.
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written
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Nicolas Rosewick
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