Microarray hybridization differential expression

In a recent publication, the largest number of AD brains to date were analyzed by microarray. Unlike the previous studies, the RNA from 61 AD frontal cortex samples and 53 controls samples were pooled, and multiple hybridization experiments took place on two-array platforms. Only 3 of the top 30 differentially expressed genes from each platform were found to be in common RGS4 and RAB3A were decreased and ITPKB was increased. However, real-time PCR with the individual samples confirmed these changes were specific to the AD patients, and these data support the evidence of disrupted intracellular calcium signaling in AD [112],... 

Despite its current widespread use and the drive toward ensuring high-quality microarray data by the implementation of MIAME guidelines, very little is known about the extent to which application of different technologies influences the outcome of transcriptional profiles and differential expression. However, microarray users should be aware of studies that have attempted to present a comprehensive evaluation encompassing different probe types (oligonucleotides and cDNAs), labeling techniques and hybridization protocols [52]. 

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