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Microarray analysis still is a powerful tool to identify new components of the transcriptosome.
Even after eliminating apoptosis, however, microarray analysis still did not show significant up-regulation (>1.5-fold over control) of REST-regulated mRNAs (Supplementary file 2 and Figure 5 figure supplement 2), suggesting that premature differentiation per se was not the sole underlying cause of the apoptosis.
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For many other yeast species however, thusfar the usage of DNA microarray analysis is still rather limited.
However, although the genomes of a number of filamentous fungi have been fully or partially sequenced, microarray analysis is still in its infancy in these organisms.
One reason is that obtaining tissue samples for microarray analysis can be still difficult.
Therefore, we restricted the microarray analysis only on those probes that were still considered as valid (Illumina in-house data, available online).
There are still other aspects of microarray analysis that can introduce variability into results, according to Weis.
While the downstream gene expression profiling techniques using microarrays are very reliable for large-scale investigations, there are still challenges prior to microarray analysis including the choice of a relevant sample type and RNA and cell isolation method.
Thus improving single-gene DEG identification algorithms still has great implication for DEG microarray analysis practice in biology.
Genes for which the expression level was not changed in a significant manner still showed a trend consistent with the microarray analysis.
Although microarray analysis has become an important tool in animal genomics, there is still the major problem that no clear consensus about the microarray data processing methods for detection of differentially expressed genes exists (Jaffrezic et al. 2007).
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