Effect Of Methylation On Transcription Factor Binding Sites
Hello there, we have methylation array data which gives us a number of sites that are relatively hyper- or hypo-methylated in cases relative to controls. We want to determine the net effect of these changes in methylation on gene expression. I am aware of some eQTL resources for doing this, but wondered about any tools specifically for examining the net effect of methylation on transcription factor binding sites. Can this be done with Jaspar or other tools? What analysis would you recommend?
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I'm confused a bit. Is your primary concern the effect on gene expression or on transcription factor binding? They are related conceptually, but the analyses and data inputs would, I think, be pretty close to orthogonal for the two different questions.
I'm also confused, for the same reason. First you say "effect of these changes in methylation on gene expression", then "effect of methylation on transcription factor binding sites." Which is it? The analyses would be quite different.