Seventeen measurements reported an increase in DNA methylation by the qPCR method that was not detected by the microarray method (approximately 15% false negative rate in the microarray experiment).
This method allowed identification of more than twice the number of canonical pathways determined by the microarray method and seven times more than by proteomics (Fig. 1B).
IPA analysis of the genes detected by the microarray method identified 35 canonical pathways (Fig. 1B) and numerous biofunctions (Supporting Table 1).
We found no evident methylation change in samples treated with furan for 4 weeks compared with control samples by the microarray method.
In Figure 4, we show the ratio of the expression level estimated by the abundance within the EST database method [ 22] to that measured by the microarray method [ 24, 25].
Thus, we define the correlation coefficient between the two measurements as where the average is over all genes present in both datasets, δ fmicroarray = fmicroarray -, δ fEST = fEST -, fmicroarray is the expression rate measured by the microarray method, and fEST is the expression rate measured by the abundance within the EST database method.
A comparison of the genotype/subtype results obtained with the two methods is shown in the table 2. Seventy-four of the 78 samples previously tested by Versant™, were successfully genotyped by the liquid microarray method (74/78, 95%).
With over 200 cells measured by metaphase karyotype and 459 cells measured by the PS microarray method, we found that the per-cell accuracies of the methods are roughly in line.
To explore the conserved features and shared genomic contents, Salama et al., in 2000, attempted to determine the core set of genes in 15 H. pylori strains by microarray method and observed that 1,281 genes are shared by all the examined strains.
