In this respect, the global approach in our study to assess the expression data in the manifold of metastatic tumors, all in the screening phase by microarrays, in the validation phase by RT-qPCR and response validation by target protein expressions and their miRNA dependent regulation, as mentioned above, proved to be advantageous.
To validate the results obtained with the microarray data, we assessed the expression for the six key genes of the subnetwork along with TWIST1 in RNA-Seq data available for 178 out of the same 197 patients of the TCGA microarray data set.
Two observers without knowledge of the clinical data independently assessed the expression of PRAME.
The approach allows us to assess the quality of the expression data and is more rigorous than spot-checking a random collection of genes.
In addition, it allowed to set a quality standard as well as to assess sources of errors in the expression data.
To assess drought-driven transcriptome responses, the expression data of drought-treated trees were compared with their respective controls within organs and genotypes.
The quality of the expression data was assessed using the Refiner module of Expressionist.
As an initial validation of our hypothesis that GWASs and microarrays tend to identify the same genes, we used a meta-analysis of the Oncomine gene-expression data to assess the expression of the GWAS-identified genes (Table 1).
We therefore decided to validate the array data by assessing the expression of RhoC at the level of message RNA and protein in the HCC samples.
We further examined previously published microarray data to assess the expression profiles of ABC genes in two spider mite strains, MR-VP and MAR-AB, that are resistant to multiple pesticides [ 42].
These questions can be answered by assessing the expression levels (as indicated by RNAseq data, see further details in next section) of genes encoding proteins predicted to have surface location, thus allowing us to compare the surface protein composition from both African parasites.
