DS-ALL gene expression profile. (A) GSEA analysis on ICH dataset. Genes are ranked (bottom of panel, gray) according to their expression in DS-ALL samples versus the rest of the samples, by GSEA, using the default parameters. The members of a gene set S (here, the set of 535 genes down-regulated in DS-ALL, AIEOP data) are tested: are they randomly distributed in the ranked gene list, or primarily found at the top or bottom? Occurrences of members of the gene set S in the ranked gene list are shown as vertical black lines above the ranked signature. The green curve and upper y-axis represent the enrichment score (ES) as a function of the number of ranked genes tested for enrichment of gene set S. See supplemental Methods for full details. (B) Expression levels of the genes from the refined DS-ALL lists, measured on the AIEOP dataset. Four hundred twenty-three probe sets that belong to the refined DS-ALL profile gene lists are centered and normalized. Values for each individual case are represented by a color, with red representing deviation above the mean and blue representing deviation below the mean. The colors along the x-axis represent the different ALL subtypes, listed on the right of the plot. DS indicates Down syndrome ALL; HD, high hyperdiploid; TEL, TEL-AML1; BCR, BCR-ABL; E2A, E2A-PBX1; and MLL, MLL-AF4.