Several genes were selected, including light-harvesting chlorophyll a/b binding protein (LOC_Os03g39610), starch and sucrose metabolism pathway related proteins such as glycogen/starch synthases (LOC_Os07g22930), 4-alpha-glucanotransferase (LOC_Os07g46790), and Glucan water dikinase (LOC_Os06g30310).The real-time RT-PCR results mostly matched the microarray expression patterns.
Consistent with our microarray results, wherein several probes corresponding to C3AR1, CAMP, CCL5 and IFNγ exhibited a down regulation along with up regulation of C4BPA, real time PCR results also matched the microarray expression profile (Supporting Table S2 in Additional file 1).
For a matched miRNA and mRNA microarray expression data set, the miRNA and mRNA clusters correspond to groups of DE miRNAs and mRNAs, respectively, which are present in the miRmR map matrix.
We considered a short timecourse data set comprising matched miRNA and mRNA microarray expression data.
We used a second data set, a timecourse study with matched miRNA and mRNA microarray expression profiles, to illustrate our module-identification method.
For each gene, scaling parameters were found by identifying the 5th and 95thpercentt quantiles of expression in RNA-Seq and microarray and then linearly shifting microarray expression to match these quantiles with RNA-Seq (see Figure 5A).
A similar trend analysis shown in Figure 5A is also performed by comparing human and mouse microarray expression data in matched tissues.
qRT-PCR expression profiles were compared with microarray expression profiles and scored as matching if they agreed at all developmental stages or if the majority of stages were in agreement and the significant changes in expression also agreed.
For example, a novel algorithm predicting miRNA targets, GenMiR++, has been recently developed using microarray expression profiles in addition to sequence matching [ 19].
Microarray expression data were generated from LCM-cell-sampled and bulk tissue-sampled specimens acquired from matched cases, for ten adenocarcinomas and six adjacent-benign samples.
