Figure 2.

Reproducible “plaid” pattern of intrachromosomal interactions in four cell types. (A) Intrachromosomal interactions along Chr.17 (1-Mb bins smoothed with a 200-kb step size). The color of each dot represents the log₂ of the normalized contact number for the corresponding genome bins. (B) Pearson's correlation map of Chr.17 at 1-Mb resolution shows chromosome compartmentalization and the characteristic plaid patterns. The first principal component eigenvector (below heat map: “A” and “B” refer to active and inactive chromatin states) identifies compartments and correlates with gene density and GC content defined isochores (in GC%: L1 < 37%; L2 37%-41%; H1 41%-46%; H2 46%-53%; and H3 > 53%).