Although transcriptional profiles in such target disease tissues/cells are ideal for such analyses, the complexity of procuring such tissue biopsies/cells and the low amount of RNA from these specimens for standard microarray assays has made whole blood, a practical and an attractive surrogate tissue in clinical research [3], [4], [5], [6], [7].
Indeed, the quality of data generated by microarray assays has been questioned [ 1, 2].
Microarray assays have been widely adopted in cancer marker exploration and expression profiling of tumor genes [ 3, 4].
To examine the results for all 60 miRNAs on one plot, we cannot simply plot qPCR Ct values versus microarray signals for all miRNAs in all tissues, because both the qPCR and microarray assays have differential sensitivities to different miRNAs.
To meet this challenge, hybridization-based microarray assays have been developed that are capable of measuring variation in the expression of hundreds-to-thousands of genes in multiple samples in a single experiment [ 12, 13].
Although Ach et al [ 41] reported good correlations (r > 0.9) in 53/60 miRNAs when comparing microarray (Agilent) and individual TaqMan qPCR assays (Applied Biosystems), they could not compare all 60 miRNAs in one plot because qPCR and microarray assays have differential sensitivities to different miRNAs.
Because the fluorescent dyes used in most microarray assays have slightly different efficiencies for light emission, the detection efficiencies of the phototubes has some wavelength dependence and hence differ for the different dyes, and because the PMTs exhibit nonlinearities at high and low intensities, the log-ratios measured often exhibit some systematic, intensity-dependent variation.
Microarray assays have indicated that the gene expression profile was altered in the liver of SCD knockout mice, and the most obvious pattern was down-regulation of the genes involved in lipogenesis and up-regulation of the genes associated with fatty acid β-oxidation [ 8].
The ChIP-chip analyses also showed that only one (STM2938) of the 13 newly-identified, potential σ-dependent operons from the DNA microarray assays has a σ DNA binding site associated with it (Table 3), suggesting that the other 12 operons may be indirectly regulated by σ.
When tested with CL-fed chicken muscle tissues, the protein microarray assay had higher sensitivity (0.9 ng/g) than the ci-ELISA (0.1 ng/g) for detection of CL residues.
