We observed an increased repression of the PRDX1 3'UTR when miR-510 was expressed when compared to the scrambled controls.
681 unigenes were found to be differentially expressed when comparing the two libraries, where 400 were preferentially expressed in buttons and 281 in roots.
As many as 1751 genes in Gencode Release 19 were identified to be differentially expressed when comparing stranded and non-stranded RNA-seq whole blood samples.
Again, these three genes were found to be differentially expressed when comparing array data from stable and progressive patients; however only TRIB1 reached statistical significance (p = 0.023).
When considering sporadic and radiation-induced tumors as the two subgroups in the search for a signature, whatever the histological subtypes (FTA or PTC), a final discriminating signature of 322 genes was found to be differentially expressed when comparing the two groups.
Interestingly, in the PD 54 and PD 38 comparison, only 42 genes that showed differential promoter methylation were also affected by changes in gene expression (Table 1), while none of the genes with differentially methylated promoter regions were found to be differentially expressed when comparing the PD 47 and PD 38 cultures.
Previous studies on genome-wide expression profiling of osteosarcoma have reported lists of genes that were found to be differentially expressed when comparing tumours with a poor histological response to chemotherapy and those with a good response (Ochi et al, 2004; Man et al, 2005; Mintz et al, 2005).
A potential limitation of this study is that relatively few genes were differentially expressed when comparing the NC-rich, mixed, and CLC-rich NPs in the non-chondrodystrophic dogs, whereas in chondrodystrophic dogs relatively many genes were up- or downregulated.
Genes that show ASE exclusively in one tissue are often the genes that are differentially expressed, when comparing that tissue with all other tissues (Additional file 1: Table S9).
Indeed, a series of genes that are differentially expressed when comparing wild-type and TRIM32 knockout animals were detectable.
