In patients who developed a tumor recurrence we detected a significantly higher PTTG expression in primary tumors (median expression: 2.63) when compared to patients who did not develop a tumor recurrence (median expression: 1.29; P = 0.009).
Median expression levels when filtering at a threshold of 4 FPKM were 12.75, 12.55, 12.7, and 12.52 for autosome female, Z female, autosome male, and Z male, respectively (fig. 2 b; supplementary table S1, Supplementary Material online).
No significant association was found between hTR abundance and histological subtype or tumour grade when hTR expression was considered as a dichotomous variable; however, a trend in association of high hTR with the more aggressive subtypes and significant association of high hTR with grade 3 tumours was highlighted when median expression levels of hTR were considered.
The HIV infected group showed significantly elevated FOXP3 expression when expressed as a percentage of total CD3+CD4+ cells (median of 8.11%, range 1.33 26.27%, P = 0.002, Figure 1B,C).
However, when the median expression levels were considered, we found a trend in association, with the lowest hTR expression in those tumours of the well-differentiated subtype compared to the other more aggressive subtypes (summarised in Table 3).
Transcripts were categorized as present when their median expression in at least one experimental group was above the 5th percentile of all exonic control signals integrated on the employed Affymetrix 1.0 ST array.
When the median expression in tumor was compared with that in normal tissues, moderate increase with almost 5 fold was detected in fully blown tumors than in the non-malignant, normal samples, and those differences, based on the performed statistical test, were significant (p = 0.012).
When the log2 median expression ratios were averaged for all genes with putative hsa-mir-548 target sites, the colorectal sample had the lowest relative expression level (q = 9.72, v = 12738, k = 6, P<0.001 Tukey test; Figure 8).
This difference was statistically significant, whereas it was not when ALK mRNA median expression levels of ARMS-not and ERMS were compared (P=0.79).
However, reanalysis of multiple gene expression datasets using both microarrays and RNA-seq shows that median expression levels of X-linked genes when assayed in whole testes are in fact approximately 1.5-fold lower than those of autosomal genes (Meiklejohn et al. 2011).
