Figure 5

Changes of motif architecture and chromatin state in cell comparisons.

(A) The percentage of changes in FFL architecture based on FFL instances in corresponding source cell line (such as H1 for H1-GM12878). The values of x-axis represent the number of edges of FFLs in the end cell types. (B) FFL instances in the source cell line were divided into different groups according to the alterations of FFL structures (including edge gain, loss or no change). For each group, the percentage of FFL instances with at least one chromatin state change under different types of changes of motif structures was shown. (C) The percentage of genes involved in FFL instances with chromatin state change or not. (D) The significant biological processes enriched by genes involved in FFL instances with chromatin state change. (E) Chromatin state transition of FFLs under different types of changes of motif structures: without alteration in motif structures (E-1; F-1), loss edges from FFL (E-2; F-2), gain edges (forming FFL) (E-3; F-3). The four types of chromatin states are arranged in the same order along each axis. The I, II and III quadrants separately represent chromatin state transitions at top-, intermediate-TF and target gene of a motif in an anticlockwise direction. Each curve represents a kind of chromatin state transition. Colors of curves indicate the chromatin states of genes at the starting point of comparison (e.g., H1 in H1-GM12878). The terminal points of curves represent chromatin states at the end point of comparison (e.g., GM12878 in H1-GM12878). The thickness of curves represents the significance of chromatin state transition by the value of 1-(P-value). (G) Examples of changes of chromatin state-modified FFLs. The log2-transformed fold changes in gene expression are showed.