HOX-specific gene expression patterns are determined by the homeodomain. (A) Three independent cell lines were generated from primary bone marrow cells transformed by HOXA1, HOXA9, or the respective swap-constructs as indicated. RNA was harvested and quantitative RT PCR for Slc14a1 (NM_028122), a sentinel gene for HOXA1-transformed cells, was performed. Values were normalized for β-actin. Relative quantities are plotted as mean ± SD of a triplicate experiment. Expression levels found in the first HOXA9 transformed line were arbitrarily set to 1 unit. (B) Quantitative RT-PCR for Enpp1 (NM_008813), a gene specifically expressed in cells immortalized by HOXA9. Procedure and legend as in panel A. (C) Quantitative RT-PCR for Myb that is induced by HOXA1 and HOXA9. (D) Relationship of the gene expression program induced by parental HOX genes and the respective swap derivatives. RNA from the individual cell lines as described in panel A was pooled and hybridized to expression arrays. HOXA1 and HOXA9/1 patterns were compared with those found in HOXA9 and HOXA1/9 cells. The top 100 scoring genes with the highest expression difference and lowest variation (P < .05) were used to construct a dendrogram. (E) Clustering of the top scoring genes as in panel D. Genes are arranged as lines and RNA samples are represented by columns. The transduced HOX construct is given at the bottom. A listing of the individual expression values can be found in supplemental Table 1.