The contact matrices, correlation matrices, and difference matrices of chromosome 14 after applying normalization.

<p>(<b>A–D</b>) denote the contact matrices after removing reads mapped to multiple locations on the genome, (<b>E-H</b>) the contact matrices after applying SCN normalization method to the maps in (<b>A–D</b>), (<b>I–L</b>) the contact matrices after applying both genomic sequential distance based method and SCN to maps in (<b>A–D</b>), (<b>M–P</b>) the correlation matrices based on maps in E-H, and (<b>Q–T</b>) the difference matrices of between correlation matrices in M-P of normal and malignant samples.</p

The contact matrices, correlation matrices, and difference matrices of chromosome 14.

<p>This figure illustrates the original contact matrices, correlation matrices, and difference matrices of chromosome 14 for the normal human B-cell, human acute lymphoblastic leukemia B-cell, human MHH-CALL-4 B-ALL cell line, and human lymphoma RL cell-line. Heat maps (A-D) visualize the original number of contacts within the chromosome, (<b>E</b>-<b>H</b>) the Pearson’s correlation matrices generated from the original contact matrices, and (<b>I</b>-<b>L</b>) the absolute difference matrices generated from the correlation matrices.</p

The spatial gene-gene interaction networks and the analysis of its properties.

<p>The results were based on the contact data with reads that were mapped to multiple locations on the genome removed. (<b>A</b>) The gene-gene interaction network of genes residing in chromosome 14 for the CALL-4 cell line. (<b>B</b>) The distribution of node degrees. (<b>C</b>) The histogram of shortest path lengths. (<b>D</b>) The plot of average clustering coefficient against of the degree (the number of neighbors) of a node. (<b>E</b>) The plot of closeness centralities against the degree of a node. (<b>F</b>) The stress distribution. (<b>G</b>) The plot of topological coefficients against the degree of a node. The network and its properties were visualized and analyzed by Cytoscape <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058793#pone.0058793-Shannon1" target="_blank">[32]</a>.</p