Explanation and illustration of the "Interaction Ratio". (A) An illustration of the theoretical assumption of interaction ratios is shown here. The first part is a description of the nucleus. Strings with different colors are chromosomes. The genome has open and compact chromatin, as shown in the middle section; in the open chromatin, more random short-range interactions are easier to detect by Hi-C experiment. And the spectrum-like interaction ratio profile is displayed in the last section. (B) In part of Chromosome X, visualization of the interaction ratios and first principal component signals is displayed using the UCSC Genome Browser for Hi-C data in the GM06990 cell line. The yellow portion of the signals represents the bins with plus (+) signals; the gray portions are bins with minus (-) signals for both interaction ratios and first principal components. The two signals are quite similar. The DNase I Hypersensitive Sites Peaks were acquired here as a reference of the open chromatin. The RefSeq genes are also included in this figure. (C) A close look of a region in Chromosome X, from position 101,000,000 - 104,000,000. The first track is a snapshot of the clusters and boundaries after Markov Clustering. Boundaries between neighboring clusters are highlighted as "red blocks". The binding sites of CTCF and Pol II and the locations of transcriptional start sites are displayed to show their levels of enrichments in boundaries.