Global Chromatin Domain Organization of the Drosophila Genome
Figure 1
Visualization of chromatin domains by “domainograms”.
To visualize local enrichment of a chromatin component, we calculate a probability score for the enrichment in a window of w neighboring genes under a null model in which all genes are randomly permuted. This calculation is done for all possible windows, ranging in size from a single gene to all genes on an entire chromosome arm, and for all possible window positions. A color scale (ranging from black for non-significant scores close to 1, to red for highly significant scores <10−6, see color scalebar) is used to visualize the probability scores in a triangular graph, which we term “domainogram”. Horizontally, each score is plotted at the chromosomal position of the center of the window, and vertically the windows are ordered by size. Thus, we obtain an intuitive visualization of local enrichments at all possible scales. See Methods for a detailed description. A) Domainogram of HP1 binding on the right arm of chromosome 2. B) Genomic map of HP1 binding used to generate the domainogram. C–D) domainogram plot and corresponding binding map after random permutation of the HP1 binding values along the genome. Genomic locations (Mb) are indicated below each graph in A–B.