Gene expression profiling of prelymphomic Hdac1^Δ2/Δ2; Hdac2^Δ2/WT thymocytes. (A) Total thymocyte cellularity is similar between Hdac1^Δ2/Δ2; Hdac2^Δ2/WT (n = 5) and WT LMCs (n = 7) of 2- to 3-week-old mice used for global transcription profiling. Bar indicates mean (P > .78, unpaired t test). Hierarchical clustering of samples based on signal detection values of 8878 genes indicates a distinct transcriptional program exists between Hdac1^Δ2/Δ2; Hdac2^Δ2/WT and WT LMCs. S indicates sample. Number indicates sample identifier, and WT or mut postfix indicates samples from WT LMCs or Hdac1^Δ2/Δ2; Hdac2^Δ2/WT genotypes, respectively. (B) Summary of transcriptome profiling. Number of transcripts detected in Hdac1^Δ2/Δ2; Hdac2^Δ2/WT or WT LMCs samples (left), presented as unregulated (gray), up-regulated (up), or down-regulated (down). Functional annotation clustering of all deregulated genes using DAVID (right). Represented are the top 10 statistically enriched biologic function gene ontology terms (BF-GO terms) and the number of deregulated genes of each annotational cluster. (C) DAVID analysis was also performed on up- and down-regulated genes, identifying enrichment of gene clusters as indicated. Gene names and associated BF-GO terms are listed; colored blocks indicate a corresponding GO term association positively correlated. Gene enrichment P values are provided by DAVID; calculated using EASE Score (modified Fisher exact P value).