Moreover, for each individual LV tissue, differential methylation showed a predicted correlation to differential expression of the corresponding gene.
First, we compared differential expression based on the proteomic data with the differential expression of the corresponding mRNAs using transcriptomic data from both RNAseq [ 15] and microarray analyses [ 16] (Fig. 2).
Together, these data indicate that the regulation of genes detected by whole blood transcriptomics was translated in differential expression of the corresponding proteins in circulating blood.
As is true in general for microarray approaches, observed changes in the signal for a particular transcript may be influenced by abundance of the organism expressing the transcript, by differential regulation of the corresponding gene, or both.
The binding strength of CREB itself showed no association with the differential expression of the corresponding target gene in the hepatic feeding to fasting switch.
As a part of our analysis, we computed the MI between the differential enrichment of the corresponding gene sets and also ortholog pairs of genes in the two species.
The variation in the relative frequency of those tags, stored in databases, are then used to point out the differential expression of the corresponding genes: this is the so called "digital Northern" comparison.
Probes with a q-value of <1% were considered to indicate differential expression of the corresponding genes if the mean fold change of the sample triplicate was at least 1.5.
This analysis is based on the relation between the abundance of ESTs in a cDNA library and the differential expression of the corresponding genes [ 20, 21], and is ordinarily performed on ESTs in cDNA libraries that are not normalized [ 22, 23].
The 23 promoter mgrade-CpGs showed a significant inverse correlation between the histological grade-associated methylation change (i.e. the Spearman's correlation rho between the methylation status and histological grade) in human aortas and the differential expression of the corresponding mouse genes - i.e. APOE-null relative to WT (Pearson's r = −0.71, p = 1.5×10−4).
