The signature of VNN2⁺ALL is enriched with myeloid features and functional annotations related to immune response, interferon signaling, cell adhesion, and the JAK-STAT pathway. (A) Heat map with 1061 differentially expressed genes showing the transcriptome signature of 50 B-ALL samples ordered by increasing VNN2 RNA expression (left panel). Using edgeR,⁴⁸  a linear model was fitted across the dataset of 50 ALL samples using VNN2 expression as predictor of gene expression. Genes that showed a significant linear relationship with VNN2 expression were selected (false discovery rate [FDR] ≤0.01). Genes were additionally filtered using Spearman correlation (FDR ≤0.04). A total of 549 genes and 512 genes appeared to be positively or negatively correlated with VNN2, respectively. Genes positively correlated with VNN2 include 3 genes that were identified by proteomics in an independent cohort using CSC technology (right panels). (B) Positively correlated genes were grouped by pathways using the online tool and database ConsensusPathDB⁴⁹  (FDR ≤0.01). The most significantly overrepresented pathways (according to P value) included the immune system, interferon signaling, β-2 integrin–mediated interactions, and the JAK-STAT signaling pathway. Node size indicates the number of genes contained and the color refers to significance (P value). Two nodes are connected by a line if they share members. The line width reflects the relative overlap between the nodes, whereas the line color represents the number of shared members that are also found in the input. (C) Enrichment plot for the myeloid signature obtained after performing gene set enrichment analysis.⁵⁰  (D) Components of the VNN2⁺ ALL signature generated using the Genomatix genome analyzer reveal functional annotations related to myeloid cells and their cellular location (adjusted P ≤ .05; P ≤ .01). Lines between genes indicate a functional association. The line type indicates the evidence level. Dashed lines indicate a functional association based on cocitation or experimental validation. Solid lines indicate a functional association based on expert curation. Diamonds indicate that a gene carries a binding site of the associated transcription factor. Arrows indicate that a gene is altered by the associated gene. Curved lines indicate that a gene alters itself on a transcriptional or protein level. The line type indicates the evidence level. Myeloid_DN, myeloid gene expression signature; NES, normalized enrichment score.