ChIPSeq Co-Localization

Question

[William]

Hello,

Does anyone have any tips on how to do co-localization analyses on a handful of transcription factors? I see how to do everything up to peak-calling, but after that i'm not sure how I would go ahead analyzing co-localization.

Thanks!

[LChart]

Are you asking how to identify regions where multiple transcription factors are binding? You can use bedtools intersect on the peak files to find overlapping peaks. What kind of biological questions do you have? Are there multiple conditions?

[William]

Yeah, exactly... I just want to know where a set of transcription factors have overlapping peaks. There are no conditions. As far as a biological question goes, I want to know if these transcription factors are co-enriched at the promoters of genes responsible for centriole biogenesis.

[LChart]

OK cool. So you can still use bedtools intersect and bedtools overlap to find peaks (or extent of overlap) between TF binding peaks and (using a centriole_biogeniesis_promoter.bed and non_centriole_promoter.bed) overlap with centriole and non-centriole promoters. You can then set up a Fisher's exact test via the table

                       co-bound peaks        not co-bound peaks
centriole-promoter                  A                         B 
non-centriole-promoter              C                         D

[William]

Ah thanks so much, super helpful!