Global gene expression and genomic analyses of pre-TCR–deficient and pre-TCR–proficient TEL-JAK2 T-cell leukemias. (A) Representative unsupervised hierarchical clustering of TEL-JAK2 (TJ, light-blue), TEL-JAK2/Rag2^−/− (TJR, dark-blue), and Ikaros^L/L (T, yellow) tumors and wild-type (WT, pink) and preleukemic Ikaros^L/L (Ik, red) thymocytes using the top 5% most varying probe sets (n = 354) across all 25 samples, resulting in 3 major groups (C1, C2, and C3). Hues of red and blue indicate higher and lower levels of relative fluorescence signal, respectively. Samples and genes were clustered using the Ward linkage and 1-Pearson coefficient of correlation as the distance metric. Sample annotations indicating the tumor samples (T in black box) and nontumor (W in white box) samples are shown below the sample dendrogram. P values correspond to a global Fisher exact test. Gene clusters are labeled a to e. (B) Array-based CGH ideograms of 5 TEL-JAK2 (TJ2), 3 TEL-JAK2/Rag2^−/− (TJ2/Rag2^−/−), and 6 TEL-JAK2/Ptcra^−/− (TJ2/Ptcra^−/−) tumors. Chromosomes are listed in numerical order from left to right. Red squares above zero on the y-axis represent genomic gains (ratio > 1.2), whereas green squares below zero indicate losses (ratio < 0.8) relative to the diploid control. The yellow squares indicate the absence of numerical alterations relative to the diploid control. X chromosome profiles should be discounted because some lymphomas were derived from female mice and the reference DNA was obtained from a wild-type C57BL/6 male mouse.