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The gene expressions in leukemia samples were normalized with the housekeeping gene GUS as an endogenous control and the expression levels were calculated relative to pooled normal bone marrow (Table 3).
Analysis of the selected Hox A cluster and Hox cofactor genes revealed a high degree of co-expression between these in leukemia samples, where correlation coefficient between HOXA5, HOXA7, HOXA9 and MEIS1 ranged between 0.83 and 0.92 (Spearman rank correlation, p<0.0001 in all cases, e.g. in Figure 3A).
ABL1 was chosen as the endogenous control based on its documented expression and stability in leukemia samples.
In order to assess the frequencies of mature DCs in leukemia samples, we therefore used a second immunophenotypic panel.
Among these the CC genotype of the c.553G>C (rs1805794) polymorphism was more frequent in leukemia samples, but the results were not statistically significant (p=0.0534).
PyClone (v.0.12.3) was downloaded (http://compbio.bccrc.ca/software/pyclone/) and used to estimate the number of clones in leukemia samples from each patient.
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To our knowledge this is also the first study that measured FLT3 receptor expression levels in conjunction with signaling profiles in primary leukemia samples.
Using these parameter values, we found 32 support vector samples in 72 leukemia samples and 44 support vector samples in 102 prostate cancer samples.
Similar association was not apparent in our leukemia samples, and no correlation was noted with overall survival in this study, probably due to the sample size, or due to the differences in cancer type.
Tissue microarrays (TMAs) are useful for high-throughput analysis of protein expression of target genes in acute leukemia samples and for validation of gene microarray analysis.
Consistent with these results, FLT3, HLF and JAG2 expression correlated with HOX A cluster gene expression in human leukemia samples.
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