FANTOM5 enhancers: intepretations

Question

[c.clarido]

Hello community,

I have recently downloaded a melanocyte-specific FANTOM5 Human Enhancer Tracks (http://slidebase.binf.ku.dk/human_enhancers/presets). The fist 4 lines of the bed file looks like this:

chr1    1014834 1015095 chr1:1014834-1015095    0.034   .       1014858 1014859 0,0,0   2       1,213   0,48
chr1    2574343 2574764 chr1:2574343-2574764    0.012   .       2574704 2574705 0,0,0   2       332,29  0,392
chr1    6088225 6088518 chr1:6088225-6088518    0.03    .       6088327 6088328 0,0,0   2       85,173  0,120
chr1    7764543 7764931 chr1:7764543-7764931    0.02    .       7764716 7764717 0,0,0   2       133,174 0,214

Each predicted enhancer is described in BED12 format (columns 1-6 as chromosome, start coordinate, end coordinate, enhancer ID, score and strand) with two blocks denoting the merged regions of transcription initiation on the minus and plus strands. The thickStart and thickEnd columns denote the inferred mid position. The score column gives the maximum pooled expression of TCs used to construct each bidirectional loci.

I am interested in using this BED as custom annotation using VEP. However, I am not sure how to interpret the the BED file. How do I know if the variant I am looking at falls within an enhancer region? Can I see that from the given scores? If so, how would you interpret the scores?

Thank you very much in advance.

Answer 1

[Kevin Blighe]

You can assume that the enhancer region is defined by the first 3 columns. I assume that 'TCs' refers to 'tag clusters'; so, the higher the number, the greater the activity of the enhancer region.

By the way, FANTOM6 is coming out: https://www.biorxiv.org/content/10.1101/700864v2

Kevin

[c.clarido]

Thank you Kevin!

I assume that 'TCs' refers to 'tag clusters'; so, the higher the number, the greater the activity of the enhancer region.

Do we look at the last column or the 4th column for scores? and are there any cut-offs?