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The success of previous two-transcript diagnostics shows that, despite being formulated using microarray platforms, these intrinsically simple classifiers can be implemented efficiently through pre-existing gene expression methodologies.
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We identified orthologous relationship for 3.861 genes across the microarray platforms of these two studies based on the best reciprocal BLASTN hit between cDNA sequences and identical mapping of cDNA sequences to gene IDs (see Methods).
The reason for this difference in the two data sets is likely due to the difference in microarray platforms used in these studies.
Agilent 8x60K microarray platforms were used for these transcriptome analyses (Xuan et al. 2013).
These microarray platforms differ in their probe design, hybridization protocol, labeling and production methods [4], [5].
Using these microarray platforms, significant differences in gene expression and alternative splicing between human populations were identified [5] [9].
Our predictions of target concentration on these microarray platforms equal or outperform those made using models that rely on individual free parameters for each probe.
Notably, several recent studies using the International HapMap Project (http://www.hapmap.org/) [2], [3] lymphoblastoid cell lines (LCLs) demonstrated the utility of these microarray platforms in profiling gene expression and dissecting the genetic architecture of gene regulation [4].
The newly released genotypic data from the 1000 Genomes Project provides an opportunity to systematically evaluate the potential influence of common genetic variants on these microarray platforms for their use in human samples.
Expression measurements for 2,440 MPSS differential transcripts could not be confirmed using any of these microarray platforms.
All these microarray platforms were based on PCR amplified probes prepared from selected IMAGE consortium cDNA clones.
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