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The observed increasing trend in the number of miRNAs with log2 intensity >1 through the RA time-course and the numerous examples of miRNAs with low intensity values that show agreement in expression profiles with other cluster members, demonstrated the ability of the microarray to detect differences at low intensity.
All three had good agreement in expression levels detected by the two techniques (Table 3). 1.
These correlations reflect the observed agreement in expression levels determined by the two technologies.
We identify thousands of genes that are differentially expressed across tissues in D. yakuba and D. simulans, with roughly 60% agreement in expression patterns of orthologs in D. yakuba and D. simulans.
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While they considered the agreement for the overall expression profiles, we focused on the agreement in expressions at the gene level.
Otherwise, there was good agreement in the expression levels detected by RNA-seq and qRT-PCR (Additional file 5).
The Bland-Altman method [ 37] was used to assess the agreement in gene expression obtained by using microarrays and qPCR for the selected genes.
In the callus tissue two miRNAs (miR396 and miR399) and their corresponding target genes (growth regulating factor 4 and ubiquitin-protein ligase respectively) showed no agreement in their expression profile as expected.
Correlation coefficients for each array comparison were high, ranging from 0.8452 to 0.9604, showing good agreement in gene expression values between array hybridizations, suggesting that SMART amplification of the cDNA was not affecting representation of transcripts.
In the boxed areas in Figure 1, there is a clear agreement of peaks in expression and GC level, an agreement that can also be seen along most of the chromosome.
In agreement, TNF expression in lung biopsies of IPF human patients was localized mainly in alveolar epithelial cells [11], [12], which, in independent studies, exhibit strong labeling of fragmented DNA [44] and were shown to express a variety of apoptotic proteins and markers [45], [46].
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