Fig. 6

Integrated analysis reveals ncRNA stem cell signature in AML and HSCs. a Heatmap of pediatric AML subtype-specific fingerprint ncRNAs. b Two-dimensional t-SNE plot using 1877 variance-filtered ncRNAs. The clusters were called by densVM and correspond to 11 healthy populations and 4 AML clusters. c Standardized pathway activity scores³⁴ of the myeloid (x-axis) vs. HSC-specific expression program (y-axis) as defined by our resource. Samples belonging to the SC-AML I and II clusters are indicated by gray ellipses. d SOM-expression portraits obtained using 7094 variance-filtered ncRNAs as input. Shown are three healthy cell populations (top) including HSCs (top left)—which are characterized by high expression of Spot A and B metagenes (corresponding to 1215 and 300 ncRNAs, respectively)—and AML samples displaying high expression of Spot A or Spot B metagenes. All samples are shown in Supplementary Fig. 9. e Expression profiles of Spot A metagenes (above) and Spot B metagenes (below) across all samples. f Pathway activity scores³⁴ for the HSC-specific expression programs in “Spot A” and “Spot B” AMLs. P-value was calculated using the two-tailed Welsh’s t-test