Fig. 3

A CoolBox figure representing differential interactions of Hi-C contact matrices. Shown Hi-C and RNA-Seq data are produced from the process of hematopoietic differentiation [24]. Its clearly that there is a topological association domain (TAD) formation at the Abca13 gene region and its RNA expression is up-regulated at the same time after the differentiation. A The widgets panel of CoolBox browser, used for zooming, sliding, and locating the genome region. When moving to a new region, the figure draw bellow will be updated automatically. B Hi-C track of short-term hematopoietic stem cell (ST) shows the contact map of ST sample. The color bar indicates the normalized value of the contact map. C Hi-C track of granulocyte (GR). D Differential contact interaction result of the Selfish algorithm [16] on ST and GR Hi-C contact map. The color bar indicates the q-value (BH adjusted p value) produced from the DCI analysis. Darker color means this interaction has a lower q-value; that is to say, two contact maps are more diverse at this location. E Hi-C Diff track. It shows the difference between GR and ST’s z-score normalized contact matrices. The red region of the matrix indicates where GR has a more significant contact frequency compared to ST, and the opposite for blue areas. F BigWig track of ST RNA-Seq data, showing the RNA expression level of ST in this region. G BigWig track of GR RNA-Seq data. H A gene annotation track shows the corresponding genes within this genomic region