Association of factors with hypomethylation during RBL to LCL conversion. (a) Significant enrichment of predicted transcription factors (TFs; TRANSFAC motif) in hypomethylated regions. The 500-bp region around the center of significantly hypomethylated CpG sites was tested. Color intensity in the heatmap cells represents FDR P-values. Redder and yellower colors indicate greater and lower significance, respectively; gray indicates insignificance. (b) Venn diagram showing overlap of NF-κB targets from ChIPseq (considering targets that are also within the hypomethylated list) and hypomethylated genes (the 131 overlapping genes are listed in Additional file 4). (c) Three examples showing NF-κB p65 binding to the region neighboring the hypomethylated CpGs. The binding motif location is presented as a horizontal green bar. Below, NF-κB p65 and RNA polymerase II (Pol II) binding from GM12878 ChIP-seq data are shown. (d) Venn diagrams showing overlap between hypomethylated genes and transcription factors EBF1, IRF4, MEF2A, MEF2C, PAX5, PU.1, RBPJ, RUNX and EBNA2.
Hernando et al. Genome Biology 2013 14:R3 doi:10.1186/gb-2013-14-1-r3