Calculate statistically significant enrichment score for a specific transcription factor

Question

[ancient_learner]

Hi Everybody

I have chip-seq data of few trancription factors. I want to see whether any of those factors are significantly enriched genome-wide. (when compared to others). I also want to see their enrichment in another celltype and confirm the specificity.

Answer 1

[ivivek_ngs]

For the first part of your question , I would like to say that you can always upload your coverage tracks and peak bed file for your specific TF in UCSC or even ENSEMBL Regulatory build , and compare them with ENCODE data or other data from cell lines for human and mouse. UCSC also holds for other species, in this case you will be able to track for the enrichment signals of your TF for a specific region in the genomic browser genome wide and also if for other ENCODE data for cell lines or other experiments if you have the some enrichment in those region or not.

Note: I am guessing you are working with human or mice, if you are working on any other genome build please specify.