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Between five and eight kinetic traces were collected and averaged for each time course.
For each time course dataset, Network-Identifier enumerates all possible regulatory forms on each target gene.
For each time course, each SNP was classified for its position in the genome.
Mean velocities were extrapolated for each time course and plotted as a function of either ATP or RNA concentration.
Spearman correlations between the replicates for each time course after drug treatment in either the gene body or promoter regions.
Pearson correlations between the replicates for each time course after drug treatment in either the gene body or promoter regions.
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Samples were collected for RNA-seq every hour for the first half of each time course, and every two hours thereafter.
Samples were collected hourly for the first half of each time course and every other hour thereafter (Additional file 1: Table S1).
Suppose that the times of peak expression in the cell cycle are calculated for each gene in each time course.
They expressed the time of peak expression for each gene in each time course as a percentage of the elapsed cycle, after aligning the various time courses.
Linear fits were obtained for each time-course.
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