Figure 2
From: Chromatin states modify network motifs contributing to cell-specific functions
The landscape of chromatin state-modified motifs and their contribution to target expression.
(A) Over-represented chromatin state compositions associated with network motifs in four cell lines. Asymmetric, partially and globally symmetric motifs are shown from left to right. For the symmetric motifs, only one of possible combinations of chromatin states was displayed. Chromatin states of gene promoter in each type of motif are shown in the order of top, intermediate and bottom positions. Values are presented as the number of chromatin state compositions. (B) Examples of FFLs in type I (both of top and intermediate TFs having repressive effects on their targets) can lead to expression differences of target genes (Wilcoxon rank-sum test). (C,D) Significant differences in expression, protein levels69 of targets between different chromatin state compositions within type I FFLs in H1 cell line. Color intensities (blue) correspond to P-values of Wilcoxon rank-sum test results. Gray entries represent data unavailable. Colored rectangles indicated the chromatin states of genes at top, intermediate and bottom position in FFLs. (E) Two examples of FFLs before and after knockdown of EZH2 in HepG2. Promoters are analyzed for the distribution of histone modifications (such as H3K27me3 levels before and after EZH2 mutation in HepG2 and DLBCL cell lines: DLCL2, KARPAS-422 and Pfeiffer) and TF binding signal. E-3 shows fold-change expression of FFL instances after EZH2 knockdown (colors of bar indicate their chromatin states). (F) Two examples of FFLs in H1 cell line after EZH2 knockdown in GBM stem cell. Promoters are analyzed for the distribution of histone modifications and TF binding signal. F-3 shows fold-change expression of FFL instances after EZH2 knockdown (colors of bar indicate their chromatin states).
