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The major expression pattern among the up-regulated genes (that is, dcl-1/2, ago-1 and rdrp-2-dependent) is expected from a direct regulation by ex-siRNAs of class I, as it is the case for two of the identified genes (ID115001, ID82197) (Additional file 1: Table S1), which correspond to class I ex-siRNA-producing loci [ 20].
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The k-means clustering of differentially expressed genes identified four major expression patterns or clusters.
K-means clustering of differentially expressed genes identified four major expression patterns displaying distinct temporal profiles.
Hierarchical clustering of differentially expressed genes segregated by gestational age revealed two major expression patterns: genes induced with time and genes suppressed with time (Fig. 1c).
miRNA expression profiling revealed four major expression patterns that correlated with the known function of regulated miRNAs.
Some of these genes clustered into two major expression patterns.
We also analysed the correlation between the three major expression patterns of BARD1 with clinicopathological variables.
Across the 12 clusters, there were five major expression patterns: Group 1 contained transcripts up-regulated early (clusters 4, 8).
Eventually the normalized expression data were transformed to a logarithmic scale (log2) and subjected first to hierarchical clustering using Genesis software [ 31] to find the major expression patterns.
As shown in Figure 4, four clusters encompassing 53 genes (75%) represented the major expression patterns of P. sojae bZIP candidates.
Two major expression patterns of cell cycle related genes in M4 M6 were: (I) a pronounced peak in M5; and (II) upregulation in M4 followed by a decline in M5 and reversion in M6.
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