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Because of the complex regulation, coexpression analysis based upon microarrays does not link MITF to its known target genes in different cell types.
For example, mRNA expression analysis with microarrays does not account for regulation of gene expression at the level of mRNA stability, processing, and protein post-translational modification levels 23.
Second, RNA hybridization to human protein microarrays does not require large-scale cell culture for protein isolation and mass spectrometry, and hence it is far less laborious than current RNA chromatography techniques.
Yet, detection of antisense transcription by conventional double-stranded cDNA microarrays does not strongly distort the relationship between expression profiles of the analyzed samples compared with those obtained from pure sense signals.
It must be mentioned here that gene expression profiling by microarrays does not provide information about rates of transcription but measure mRNA abundance which might have been modified by processes such as reduced RNA degradation.
The main disadvantage of this technology is that the design of the PhyloChip, and in general of the DNA microarrays, does not allow the discovery and the characterization of novel taxa.
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However, microarrays do not perform well on formalin fixed paraffin embedded tissue (FFPET).
That Affymetrix microarrays do not effectively discriminate between different but closely related duplicated genes has been suggested for allopolyploid wheat [39].
Since Microcebus murinus microarrays do not exist, we decided to use Affymetrix human genome chips since recent studies have illustrated the feasibility of detecting non-human primate brain transcripts using human genome chips [15] [18].
Microarrays do not measure gene expression in absolute units.
In addition, microarrays do not provide quantitative measures, and are therefore not very precise or accurate.
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