Graph statistics reflect decrease in information transmission efficiencies in chromatin contact networks (CCNs) in cancer. (A) We performed network inferences on Hi-C matrices (see in Methods). The element kij is the contact strength between the ith locus and the jth locus in sequential order. Then we characterized graph statistics including betweenness centrality (BC), average shortest path length (ASPL), and closeness centrality (CC). (B) Logarithm plots of expected BC at various sequential distances for normal colon (blue) and tumor (red) samples from four individuals. (C) Boxplots showing logarithms of sequential distances of cancer- or normal-specific edges in colorectal cancer (CRC) and T-cell acute lymphoblastic leukemia (T-ALL). (D) Differentially expressed gene (DEG) enrichment in edges with different levels of BC fold change (FCb) for CRC. The enrichment was quantified as the observed/expected value of DEG ratio in edges. Edges were stratified into 200 groups according to FCb rank. The x and y coordinates of points are group averages of FCb and DEG enrichment, respectively. (E) Boxplots showing ASPL in cancer, cancer cell lines, and corresponding normal controls for CRC (left) and T-ALL (right). (F) Boxplots showing average CC in cancer, cancer cell lines, and corresponding normal controls for CRC (left) and T-ALL (right). Identification of normal- and cancer-specific edges and graph statistics including BC, ASPL, and CC were performed on the intrachromosomal CCN of Chromosome 1. In each boxplot, the center line, the bottom hinge, the top hinge, and the whiskers indicated the median, the 25th percentile, the 75th percentile, and 1.5 times the interquartile range (IQR) of each data set, respectively.
