Diffusion-enhanced characterization of 3D chromatin structure reveals its linkage to gene regulatory networks and the interactome

Passage of gene–gene interplay from genomic level to transcription and protein levels in colorectal cancer. (A) The distribution of transcriptional Pearson correlation under different C_TG distance of the whole chromosome; the color of each line indicates the corresponding C_TG distance. (B) The distribution of C_TG distance under different Pearson correlation of the whole chromosome; the color of each line indicates corresponding Pearson correlation coefficient. (C) The distribution of correlation of gene pairs with csGGIs and overall background. (D) Distribution of C_TG contact probability for gene pairs with (blue) and without (orange) gene fusion events reported in FusionGDB2 data set. (E) Distribution of C_TG contact probability for gene pairs with (blue) and without (orange) similar biological process reported in HumanNet. (F) Distribution of C_TG contact probability for gene pairs with (blue) and without (orange) PPIs reported in STRING database (G) The proportion of intra-chromosomal gene pairs with STRING PPI at different C_TG distances in the tumor sample. The proportion refers to number of gene pairs with PPIs at fixed C_TG distance/number of all gene pairs at fixed C_TG distance. The background refers to number of gene pairs with PPIs/number of all gene pairs at all C_TG distance. (H) The proportion of inter-chromosomal gene pairs with STRING PPI at different C_TG distances in tumor sample. (I) The gene network integrates colon cancer–related gene–gene interplay at the DNA, RNA, and protein levels. The three kinds of edges indicate gene–gene interplays at three levels.