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Figure 4 | BMC Genomics

Figure 4

From: Genome-wide recruitment to Polycomb-modified chromatin and activity regulation of the synovial sarcoma oncogene SYT-SSX2

Figure 4

Hierarchical clustering of differentially regulated genes. Signatures for each differentially regulated gene were derived from the extent of overlap between SYT-SSX2 peaks and the epigenetic markers within the gene body or in 5Kb bins upstream of the TSS up to -50Kb (defined as coverage ratio; each bin has a coverage ratio for each epigenetic marker). Signatures were used as the input for hierarchical clustering using Cluster 3.0. Heatmaps were generated using Java Treeview. Each row represents a gene, and each column represents an epigenetic marker for a given bin (for example H3K27me3 from 0-5Kb or PolII in gene). Coverage ratios range from 0-1 with black squares representing bins with a ratio of 0 and red squares representing a ratio of 1. Top panel: Clustering of upregulated genes. Inset is enlarged portion of the heat map, and the epigenetic markers included in this region correspond to H3K27me3 at all distances and within the gene. Gene names are listed to the right. Highlighted in red are genes that are involved in neural development and function. Bottom panel: Clustering of downregulated genes. Yellow and blue ovals isolate 2 distinct clusters corresponding to genes with SYT-SSX2/H3K27me3 overlapping regions and SYT-SSX2 peaks overlapping with modifications associated with transcriptional activation, respectively. The position and identity of the epigenetic marker(s) comprising a particular cluster are listed to the right.

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