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A pathway-based analysis thus can reveal biologically relevant similarity between results of different microarray studies even though the gene contents of the microarray platforms used do not match exactly.
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It is notable that of the four published miRNA microarray studies of ovarian cancer [17] [20], even the most comprehensive of the array platforms was limited to 470 human miRNAs and star forms [17], while the current release of miRBase (release 12.0) [22], [22] contains 969 human miRNAs and star forms.
Yet even where microarray studies have been conducted, their data remains only nominally accessible to those with sufficient means, experience and time to extract useful information.
Microarray studies have also been shown to demonstrate significant variations even under the same experimental conditions.
Microarray studies with brain specific HIF-1α knock out mouse even show that HIF-1α is dispensable for the hypoxia response[ 31].
A supervised, pathway based analysis can reveal biologically relevant similarity between results of different gene-expression studies, even if studies have used different microarray platforms with different probes and probe content.
For instance, this approach can be used in microarray studies to accurately identify the most important subset of polymorphisms even when the number of variables greatly exceeds the number of participants.
Further improvements in FFPE sample handling and new amplification approaches hold promise for even better performance of FFPE samples in future microarray studies.
Additional information can be found in part 10 of the Additional File 3. Finally, MADMuscle allows the identification of genes that change repeatedly in different studies, even when the studies are on different species or microarray platforms.
However, cell population assays such as biochemical measurements or microarray studies can be misleading as large cell-to-cell variations are often observed, even in seemingly uniform populations.
In agreement with our previous microarray studies, we found intense staining for E-cadherin and beta-catenin in adherens junctions even in high-grade cervical lesions.
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