Gene expression profiling of early HOXA9 gene targets. (A) Western blot analysis shows HOXA9 protein expression in transfected U937, K562, and Jurkat cell lines 24 hours after transfection with GFP (HOXA9–) or GFP/HOXA9 (HOXA9+) expression vectors. (B) Comparison of HOXA9-modulated transcript expression patterns between cell lines using the Eisen hierarchical cluster analysis.22 The cluster contains 141 known genes with a minimum of 3 data points that were at least 2.5-fold up- or down-regulated. Red indicates induction, green indicates repression, gray indicates excluded data, and black indicates no change. Genes were grouped into smaller clusters showing similar expression patterns: i, up-regulated in all 3 cell lines; ii, up-regulated in myeloid, no change in lymphoid; iii, up-regulated in myeloid, down-regulated in lymphoid; iv, down-regulated in all 3 cell lines; and v, down-regulated in myeloid, up-regulated in lymphoid. ▪ = AA789015, ▸ = AI234380, • = AI299780. (C) Genes exhibiting the greatest magnitude of change by HOXA9 in each cell line. Red indicates gene activation; green indicates repression in at least 2 of 3 experiments. Gene names that are highlighted in blue were detected in CD34+ stem cells.63 Names of genes or ESTs that were identified as being statistically significant by the SAM algorithm are italicized. For U937 and K562 cell lines, the false discovery rate (FDR) was set at 10%. For the Jurkat cell line, the FDR was 46%. ▪ = AA789015; ▸ = AI234380; • = AI299780. Error bars indicate SE of mean fold change for at least 2 experiments.
