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Even in the same subclass, expression levels were varied.
The conservation of these annotations is explored among the loops included in the same subclass.
Combined with the analysis to phylogenetic evolution, the number and location of Hsf intron in the same subclass are conserved.
In consideration of putative similar functions of Hsf genes in the same subclass, 19 genes containing all subclass were selected to investigate responses to drought and heat stresses using qRT-PCR.
The α2 form is in the same subclass as ProRS, SerRS and ThrRS (subclass IIa), while the GlyRS heterotetramer groups with PheRS (subclass IIc), another α2β2 heterotetramer enzyme [ 36].
The actual number of independent hits at rRNA sites is, however, likely to be much greater than our estimate but this can only be proven with rigorous phylogenetic analysis of group I introns at different insertion sites to show that in some cases, introns in the same subclass at the same site in different species have a high probability of independent origin [e.g., [ 48, 49]].
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Even when unsupervised hierarchical clustering was performed separately, based not on signal ratios but on the presence or absence of DNA hypomethylation and the presence or absence of DNA hypermethylation, the majority of patients in Cluster BN were clustered into the same subclass (supplementary Figure S1A and B is available at Carcinogenesis Online).
Even when unsupervised hierarchical clustering was performed separately, based not on signal ratios but on the presence or absence of DNA hypomethylation and the presence or absence of DNA hypermethylation, the majority of patients in Cluster BT were clustered into the same subclass (supplementary Figure S1C and D is available at Carcinogenesis Online).
The cluster analysis indicated that Hsfs in the same subclasses in Arabidopsis and soybean, or maize and rice, belong to the same branch in accord with the evolutionary relationships of Arabidopsis and soybean being dicots and maize and rice being monocots.
As shown by the consensus secondary structure of the Oedogonium and Stigeoclonium psaC introns (Fig. 4), the similarity observed for these introns extends well beyond the few residues expected to be conserved in members of the same subclass and their sites of discontinuity are found at the same location within domain I (between D(i ) and D ii )).
Both belong to the same subclass, in contrast to BMP-6, which is the member of different subfamily.
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