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These genes tend to have lower p-values in both periodicity (PPer, the significance of periodical expression pattern in the cell cycle) and regulation (PReg, the significance of varied expression levels in the cell cycle) than the non-cell cycle genes (detailed definition of these p values, refer to Cyclebase [ 15]).
Based on Cyclebase, we select 599 cell cycle genes that show significant periodical expression pattern (combined p-value < 0.001).
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These genes show periodical expression patterns with peaks at certain mitotic stages.
These results indicate that these predicted genes tend to have periodical expression patterns and varied expression levels across the cell cycle.
To examine whether transcriptional level regulation can explain the periodical expression patterns, we focused our analysis on proximal genomic features: trans-features, TF binding data from ChIP-chip experiments, and cis-features, motifs profiles in gene promoter regions.
Although Cdc8 is identified as a periodically expressed gene by one of previous studies [ 42], it has only moderately significant overall P-value (p-value > 0.001) in its periodical expression patterns according to Cyclebase, and thus was not included in our positive set.
However, its expression pattern is markedly different.
Figure 3: Global gene expression pattern in pepper transcriptomes.
Eigengene expression pattern was shown using box plot.
Rbm5 has a distinct expression pattern during lens development.
The expression pattern suggests that Lgl1 positively regulates OL differentiation.
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