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Additional file 3: List of genes, mean expression profile and Gene Ontology enrichment for superclusters.
A gene was called differentially expressed if its mean expression profile exhibited an absolute log2-FC of 1 or greater with respect to the 0 hour sample.
Each plot is the mean expression profile of a module.
Multiple probes assigned to the same RefSeq ID were summarized by their mean expression profile.
Its mean expression profile is characterized by a local minimum after 30 minutes followed by an up-regulation.
It is characterized by one prototypic expression profile, called metagene, subsuming the mean expression profile of the associated genes.
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Figure 5 shows mean expression profiles for each of the groups.
Eight time-course expression profiles were simulated with the mean expression profiles graphed in Figure 2. In total, 800 genes consisting of 100 genes per cluster were simulated with 40 equally spaced time points.
Our approach is useful in comparing the mean expression profiles across different periodic patterns, making it possible to further address the fundamental issues about the interplay between gene expression and biological rhythms.
The mean expression profiles were calculated for each cluster, and the 12 gene clusters and their mean expression profiles are available in our supplemental data web page.
Four pairs of technical replicate samples were summarized by their mean expression profiles.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com