Experimental design used to generate the training set for 3D-SP. (A) Linear schematic representation of the human HOXA cluster region characterized in this study. Genes are illustrated as left-facing arrows to indicate transcription direction and highlight the 3’ to 5’ end orientation of the cluster. The 11 paralogue groups are color-coded and identified above each gene. BglII restriction fragments of the HOXA region characterized here are shown below and identified by numbers from left to right. (B) Diagram of the 5C technology. 5C quantitatively measures chromatin contacts using primers that are complementary to predicted junctions in 3C libraries. Annealed 5C primers are ligated with Taq DNA ligase and products are amplified by PCR using oligos recognizing the universal tails of 5C primers. In this study, amplification was done using a fluorescently labeled reverse PCR primer and amplified 5C libraries were hybridized onto custom microarrays. (C) Leukemia cell panel used to train 3D-SP. Cell lines are organized by leukemia type and MLL status. AF9; AF9 gene (ALL1-fused gene from chromosome 9), ENL; ENL gene (eleven-nineteen-leukemia), wt; wild type, AML; acute myeloid leukemia, ALL; acute lymphoblastic leukemia, EC; embryonic carcinoma. (D) Distribution of leukemia cell samples used to train 3D-SP. Left pie chart indicates the distribution of leukemias expressing either MLL fusions or the wt protein (Leukemia types). Right pie chart shows the distribution of MLL types (MLL fusion types).