Expanding BED segments as a way of customizing a track for a specific analysis purpose

One of the tracks that is used in this example is describing H3K4me3 occupancy in CD4+ cells. The raw data was generated by ChIP-Seq and published in Barski et al. Preprocessing was made by Zhang et. al The other track is the genomic localisation of all genes as defined by Ensemble. In Barski et al. it was for the first time shown that the occupancy of different histone modifications in the region surrounding the transcription start site (TSS) of genes is associated to the expression of the genes. Since then many studies have been performed based on quantification of histone occupancy in the regions flanking TSS of genes. 

Below is an example of how the Ensemble gene track can be customized to define the flanking regions of the TSS's of the genes. The counts of H3K4me3 inside and outside the TSS-flanked regions is then found using the "Analyze genomic tracks" tool.

References

Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., et al. (2007). High-resolution profiling of histone methylations in the human genome. Cell, 129(4), 823–837. doi:10.1016/j.cell.2007.05.009

Y Zhang, H Shin, J S Song, Y Lei, and X S Liu. (2008).  Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC genomics, 2008.