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Fig. 3 | BMC Genomics

Fig. 3

From: CTCF-mediated chromatin loops enclose inducible gene regulatory domains

Fig. 3

Gene content similarities and differences between ENCODE cell lines for predicted CTCF loops. a Heatmap showing similarity of predicted CTCF loop-enclosed gene content across the University of Washington ENCODE cell lines. Genes are clustered into six clusters using K-means clustering. Cell lines are clustered hierarchically based on the K-means cluster patterns, using the average linkage algorithm and Euclidean distances. Heatmap colors indicate the proportion of genes from that cluster falling within CTCF loops in that cell line. b Predicted CTCF loop gene count distributions for primary and immortal cells, for all ENCODE datasets and for the subset from the University of Washington (UW). Notches extend 1.58*IQR/sqrt(n) from the medians and roughly correspond to their 95% confidence intervals (IQR = inter-quartile range). c CTCF ChIP-seq peak count distributions for primary and immortal cells (all ENCODE datasets and UW-only datasets). d Principal Components Analysis (PCA) of cell lines based on their predicted CTCF loop-enclosed gene content (PC1 vs PC2 plotted)

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