The HOXA cluster conformation can be used to classify leukemia cell samples. (A) Averaged 5C interaction frequencies from MLL-fusion leukemia cell samples (left), cells encoding only the wt MLL protein (middle), and difference between the two MLL leukemia types (right). The data from the left panel are the average of the 5C datasets presented in Additional file 4: Figure S2A, and the middle panel contains the averaged data from Additional file 4: Figure S2B. Normalized pair-wise interaction frequencies are color-coded according to the scale shown on the bottom left of each heatmap. Numbers above and on the right of each heatmap identify BglII restriction fragments corresponding to the restriction pattern shown below the HOXA diagrams. Intersecting column and row numbers identify DNA contacts. (B) Classification results of the 3D-SP trained to distinguish between samples expressing MLL fusions and the wt MLL protein. (C) Classification results of the 3D-SP trained to distinguish between samples expressing either MLL-AF9 or MLL-ENL. For B and C, the leukemia training set shown in Figure 1C was used to train 3D-SP. Results shown are from a leave-one-out cross-validation of the 3D-SPs. The pie chart on the right of each table shows the overall accuracy of the corresponding 3D-SP. Matthews Correlation Coefficient (MCC) = 0.64.