For genes that were selected from chromosomal regions of interest and not necessarily on the basis of differential expression, correlations were carried out using data from the probe set deemed most specific for the gene of interest by the Affymetrix software (e.g. microarray probe sets designated -at are considered more specific than -s-at and -x-at probe sets).
Therefore, 'single sample predictors' (SSPs) were developed on the basis of the correlation between the expression profile of a given sample with the centroids for each molecular subtype (that is, average expression profile of each molecular subtype) [ 13, 17, 26].
The genes that appear in the prognostic list of a particular study were selected by ranking all the tested genes (for example, on the basis of the correlation of their expression values (measured over the training samples) with outcome.
To probe the cellular basis of this correlation, we have suppressed expression of the nonmuscle isoforms α-actinin-1 and α-actinin-4 and examined the contribution of each isoform to the structure, mechanics, and motility of human glioma tumor cells in culture.
A 31-gene signature was generated on the basis of their correlation with the mean expression of the entire panel of 126 genes.
The investigators first identified all QTLs associated with a classical phenotype and then winnowed the list of potentially associated gene-expression traits on the basis of their correlation or eQTL overlap with the phenotype of interest.
On the basis of the correlation between NeuroD6 and mitochondrial-related gene expression highlighted by our genome-wide microarray study (Uittenbogaard et al., 2009), we hypothesized that NeuroD6 could stimulate mitochondrial mass.
The drugs were clustered on the basis of Pearson correlation coefficients that related their activity patterns across the 10 cell lines to the expression pattern of the genes in the cell lines[ 11].
Detailed morphological, mineralogical, and elemental-composition analyses of tephras enhance the chronostratigraphic basis of this correlation.
