Two ways to plot histone modification occupancy data in relation to flanking regions of TSS's of genes

A. Create aggregation plots of histone modification occupancy data using TSS's as anchor points

The track that is plotted in this example represents 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.

This example presents two aggregation plots, i.e. plots of the occupancy profile of a track. In both cases TSS's are used as anchor points and the plot area is then extended to the  +/- 3kb flanking regions. The first example uses TSS's of all genes as anchor points and the second example uses only the genes that are associated to the gene ontology biological proces term "immune response".

The first two steps of the workflow (the embedded history below) is to extract the tracks representing the 3kb flanking areas of TSS's of all genes and of immune genes respectively. How to create such tracks is demonstrated at this Galaxy page.

In step 3 and 4 of the history the aggregation plots with the tool "Aggregation plot of track elements relative to anchor regions" using TSS's of Ensemble genes and "immune response" genes as anchor points respectively. For a description of what is meant by an aggregation plot we refer to one of the Encode publications Kundaje et al.

B. Visualize the localization of histone modifications in +/- 3kb flanking regions of TSS's of immune response genes

In step 5 of the history, a tool called "Visualize track elements relative to anchor regions" is applied to the same data as in step 5 (H3K4me1 distribution in immune response genes). The tool stacks genome browser-like displays of a track from multiple genomic regions so that the occupancy profile of the track in these regions can be compared.

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.

Kundaje, A., Kyriazopoulou-Panagiotopoulou, S., Libbrecht, M., Smith, C. L., Raha, D., Winters, E. E., et al. (2012). Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Research, 22(9), 1735–1747. doi:10.1101/gr.136366.111