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. 2023 Oct 18;52(D1):D222–D228. doi: 10.1093/nar/gkad894

Figure 2.

Figure 2.

Example of context-specific TFBS query with MethMotif 2024, focusing on EGR2 and its co-factors in HEK293 cell line. (A) The heatmap shows the percentage of highly methylated (≥90%), moderately methylated (>10% and <90%), and not methylated (≤10%) CG sites in the TF-cofactor motif and surrounding area. Each row illustrates a TF-cofactor pair, each column displays a methylation status range, and color intensity represents a CG percentage within a given location and partner pair. Boxplots display ChIP-seq read enrichment scores in the co-binding peaks for EGR2 and its partners. The co-binding percentage is further displayed as a heatmap and the corresponding paired TF-cofactor motif logo is provided. (B) EGR2 MethMotif logos build on all ChIP-seq peaks (left) and in the presence of SP2 ChIP-seq peaks (right). Stacked bars above the motif logo describe CG sites methylation status. The blue, green and orange colors correspond to low, moderate and high methylation level, respectively. (C) Pie charts categorize the genomic locations of EGR2 (left) and EGR2-SP2 (right) ChIP-seq peaks, following an order starting from promoter/transcription start sites (TSS), transcription termination sites (TTS), 5′ untranslated region (UTR) exons, 3′ UTR exons, introns and intergenic regions. (D) Listing of the main enriched GO terms associated with the genes targeted by EGR2 (left) and EGR2-SP2 (right).