When the treatment response was weak, Affymetrix microarrays detected more DEGs than NGS.
Notably, three genes (YPL122C, YCL040W and YPR149W) were proven to be up-regulated during weak acid induction using microarray analysis [40].
However, the separation is less obvious with an AUC value of 0.62 (Figure 5A B), which ranked it as a relatively weak candidate in our microarray-based discovery phase.
Overall, the measured microarray responses were weak.
Although we identified various genes involved in the formation of the central nerve system using subtractive hybridization, the signal intensity of these genes in the microarray analysis was weak due to the low concentration of mRNA from the brain.
Experiments with closely related bacterium Actinobacillus suis showed only weak hybridization to the AppChip2 microarray, suggesting that the nucleotide sequence identities for the ORFs are low; consistent with earlier DNA-DNA hybridization studies [ 32] (data not shown).
For example, the SYNZIP18 SYNZIP21 pair showed no signal on the coiled-coil microarrays and showed weak interaction in FP studies (Kd > 250 nM).
Prostate, the tissue category with the second highest total number of tags, showed good correlation between SAGEmap and TissueInfo, but the correlation between the tag-based databases and oligonucleotide microarray data was weaker (r2 of 0.09 and 0.19 for SAGEmap and TissueInfo respectively).
Interestingly, in the alveolar epithelial cells of IPF lungs MMP7 colocalize with osteopontin, and application of weakest link statistical model to microarray data indicate a significant interaction between both molecules suggesting that this interaction may have an important effect on the IPF development [ 30].
Regulation of the elongation factor 1 alpha gene in Chl 50Pb mosquitoes was the only exception observed, since the decrease of expression observed by QRT-PCR results contrasted with the weak up-regulation observed in the microarray analysis.
