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The differentially expressed miRNAs were determined by expression profiles using the OpenArray system and small RNA-Seq.
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Of these, 27 tumors were also previously analyzed by expression profiling using oligonucleotide microarrays [ 6] [Figure 1].
Protein microarrays provide means of rapidly validating the genes identified by expression profiling using DNA microarrays, at the protein level.
Thus, de novo assembly using 454 technology or a combination of 454 and shorter read technologies [ 16], followed by expression profiling using short reads seems a reasonable approach.
This high degree of sequence conservation was supported by expression profiling using heterologous hybridizations to potato cDNA arrays that showed similar expression patterns in mature leaves for all six solanaceous species.
In an earlier study, we have identified several porcine miRNAs applying a novel cloning strategy based on synthesis of concatamers [ 17] followed by expression profiling using a miRNA specific quantitative PCR approach [ 27].
In complex organisms without sequenced genomes, de novo transcriptome assembly using a longer read sequencing technology followed by expression profiling using short reads is likely to provide comprehensive identification of adaptive variation at the expression level and sequence polymorphisms in coding regions.
Dendrogram analysis was performed using Progenesis SameSpots, which grouped spots by their expression profiles using an automatic correlation analysis and hierarchical clustering.
Next, we used the Web-based on line tool IPA to identify the set of biological pathways that were regulated in our experiment by integrating gene expression profiles using gene ontology (GO).
By comparing miRNA expression profiles using samples from the microarray cohort, 39 miRNAs with significantly different expression levels were identified.
Impact of the virtual mutation on other genes was determined by computation of their expression profiles using the parameters computed previously.
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