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.
Class comparison analyses using the BRB-ArrayTools software (28) were performed on genes that differ in their expression by at least 1.5-fold from the median expression level in at least one sample.
Subsequent analysis based on fold differences identified a total of 124 genes which differed at least two-fold in expression level (compared to the median expression level) in at least three out of the 14 patients.
Strikingly however, the LUAT-associated coding genes are expressed at high levels (median expression value 3.9 FPKM; Figure 1E).
Analyses of the frequency distribution of ubiquitous and SAE-enriched RefSeq-annotated genes revealed that considerably more of the SAE-enriched gene set were expressed at lower levels (median expression level 1.8 RPKM, Figure 2E) compared to the ubiquitous genes (median expression level 8.6 RPKM, Figure 2D).
For the naive FC method, denote med g t as the median expression of gene g at time point t.
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).
Here, we report that miR-204 is a predictive determinant of outcome in neuroblastoma, with lower than median expression levels in tumours at diagnosis significantly associated with poor EFS and overall survival (OS).
For median expression we chose a set at low median (∼1), and another at median ∼3 (about the minimum in Figure 4I, J, and the maximum in Figure 4K, L).
LGALS4 expression was detected at a median expression level of approximately 30% of cells staining in benign mucinous cysts, increasing in borderline tumours to similar levels of expression as in MOC (>70% of cells; Figure 4B).
