Due to technical issues, it is difficult to identify periodically expressed genes with low expression levels based on microarray [ 4, 7].
We next looked at the overall features and timing of the expression patterns of the periodically expressed genes.
First, we use the average periodogram to assess the presence of TFs that are periodically expressed in the original microarray expression data or periodically fluctuate in activities in the inferred TF AC score data.
One alternative way to regulate periodic expression would have been to use only one phase-specific mechanism in genes that are always periodically expressed and to block periodic transcription in the appropriate conditions.
In order to identify the subset of periodically expressed genes in the resulting microarray gene expression time series data, a number of computational approaches have been proposed, including Fourier analysis [ 2, 6], partial least squares regression [ 7], Fisher's G-test [ 8], model-based method [ 9], and methods using some threshold criteria [ 10].
The proliferation-associated genes in other signatures have been selected on the basis of their periodic expression pattern during the cell cycle and include several genes that, although periodically expressed, are not involved in basic cell cycle processes [10], [37].
The orthologs of these genes with aligned MBP1 motifs were identified in S. bayanus and categorized into two groups: 1. those genes that preserved periodic expression during the cell cycle; and 2. those genes that no longer periodically expressed.
Periodically expressed targets that showed statistically significant differences in expression (false discovery rate q-value ≤0.05) in the normalized datasets of 36 summer samples were identified using the GeneCycle R package [ 39].
We also find evidence for additive regulation in that the combinations of cis-regulatory descriptors associated with genes periodically expressed in fewer conditions are frequently subsets of combinations associated with genes periodically expression in more conditions.
In this way we eliminated the possibility that the overrepresentation we saw in periodic classes was the result of genes observed as periodically expressed in at least one experiment, but that the actual assignment of genes into periodic classes was random.
