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Figure 3 | Genome Biology

Figure 3

From: Classifying leukemia types with chromatin conformation data

Figure 3

Distinct contact patterns identify MLL fusion from wt MLL leukemias. (A) Heatmap representation of the information gain scores of contacts throughout the HOXA cluster. The values are color-coded according to the scale shown at the bottom of the heatmap. Numbers on the left and right of heatmap identify BglII restriction fragments corresponding to the restriction pattern shown below the HOXA diagram. Intersecting column and row numbers identify DNA contacts. (B) Averaged interaction frequencies of 22 contacts with high information gain scores (IF values between MLL fusions and wt MLL are statistically different, P <0.01). Interaction frequencies in MLL fusion datasets are the averaged values from Additional file 4: Figure S2A, and wt MLL values are from Additional file 4: Figure S2B. Error bars represent the standard error of the mean. (C) Distribution of informative contacts for classification, and binding of CTCF and cohesin in THP-1 cells along the human HOXA cluster region examined. The y-axis shows the number of CTCF ‘Tags per 10 millions’ obtained by ChIP-seq after normalization against input, across the region characterized (x-axis). CTCF peaks are numbered from left to right (CTCF1 to 7). Regions forming contacts with high predictive power are highlighted in orange.

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