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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).
In total, 3716 genes were assigned to these six major expression patterns (Fig. 5).
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.
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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].
Major temporal expression patterns of the 3 groups of genes were analyzed by PCA.
The major gene expression patterns were identified by using the Serial Expression Analysis (SEA) tools [ 59].
There were no major conserved expression patterns between the two species in response to salt stress.
Six major differential expression patterns were identified by use of Fuzzy C-means clustering [ 49] (Fig. 2).
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