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Near the cap region the discrepancy between fold changes of G/C versus A/U nucleotides is smaller.
As showed in Table 2, the best ratio obtained between fold changes of labile and persistent transcripts on mineral water stored bacteria was obtained with 23S rRNA/rplP with a value of 20.
Interestingly, there is very little difference between fold changes of STAT1 expression between preinvasive and invasive tissues compared with the normal samples, indicating that the effects of STAT1 are already present in the preinvasive tissue.
Expression patterns of the validated KO term transcripts were similar between RT-qPCR and RNA-seq; however there was no statistical correlation between fold changes of the two techniques.
Correlation analysis using Spearman's rank order correlation indicated a strong concordance between fold changes of gene expression tested by microarrays and qRT-PCR in our study (Rho = 0.81, p < 0.0001, n = 40; Figure 2).
To verify this, we conducted quantitative RT-PCR (qRT-PCR) analysis of the expression of a selection of genes in the rat kidney (see Additional file 4) and calculated correlations between fold changes of gene expression between the rat models given by qRT-PCR and the three microarray platforms.
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Ratios calculated between fold change of the most labile and the most persistent transcripts are showed in Table 2.
Relationships between fold change of DEGs and SILAC ratio of corresponding DEPs at 4 h and 24 h were estimated by the same method.
Inspired by this finding, the relationship between fold-change of mRNAs expression and the number of corresponding miRNA regulators were further analyzed.
A comparison of these three anatomical areas from the data in Moran et al. (LSN v MSN v SFG) showed a direct correlation between fold changes in genes of dopamine receptor signaling pathway and the severity of PD neuronal loss [14].
To quantify the relationship between TA and TR and REDD1 gene status, we assessed Pearson correlation between the fold changes of the differentially expressed (397 activated and 441 down-regulated) genes in wild-type and in REDD1 KO epidermis.
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