Association between retroviral integration and gene activity in CD34⁺ hematopoietic progenitors. (A) MLV, HIV, and random integration sites were annotated as TSS-proximal when located at ± 2.5 kb from a TSS (+1), intragenic when inside a gene at > 2.5 kb from the TSS, and intergenic in any other case. Black bars represent exons of a prototype gene. Arrowheads indicate the direction of transcription. (B) Histogram distribution of expression values from an Affymetrix microarray (HG-U133 + 2.0) analysis of RNA obtained from cytokine-stimulated CD34⁺ cells. Affymetrix probe sets were reannotated with custom Chip Definition Files to obtain a single expression value for each gene. Expression levels were divided into 4 classes: absent, low (below the 25th percentile of the normalized distribution), intermediate (between the 25th and the 75th percentile), and high (above the 75th percentile). The percentage distribution of the expression values of genes targeted by all integration/random sites (all ISs), TSS-proximal sites (TSS-proximal ISs), and intragenic sites (intragenic ISs) are shown by the left, middle, or right group of bars, respectively. The number of genes belonging to each category is indicated in parentheses under the corresponding bar.