Enrichment Analysis for cCREs

Question

[alexanderturco1]

Hello,

I am currently trying to perform an enrichment analysis to see if a specific motif type is enriched in certain regulatory elements (cCREs). I have a bed file with all the cCREs and a bed file with all my motif annotations, both are genome wide annotations. I want to be able to perform some sort of statistical test (something like a Fisher test) that is suitable for a large amount of data and will tell me if these motifs are enriched in certain cCREs. What can I do? I thought of intersecting the bed files and counting intersections and non-intersections but the contingency table becomes hazy when I need the whole genome comparison. Any ideas on how to do enrichment in this case?

thanks

[ATpoint]

Use established software for motif enrichments. Homer or MEME are the two most common ones. Be aware that background is key. Genome-wide background might not be accurate depending on how these regions were defined.