The amplitude of regulation (the difference between the maximum and minimum expression values across the cell cycle) was calculated for all genes and was found to be independent of sequencing coverage for genes with more than ∼300 reads (Fig. 2B).
Using MetaCore, the top significantly enriched pathways (Minimum P = 2.786E-05) were cell cycle regulation of G1/S transition, followed by the Immune response HMGB1/TLR signaling pathway (P = 6.224E-04).
For the cell cycle analysis, a minimum of 10,000 cells per sample were analyzed with flow cytometry (TreeStar, San Carlos, CA; BioRad, Hemel Hempstead, UK).
These proteins constitute an approximate minimum set necessary to describe the mammalian cell cycle.
It may well be that the impact of cell cycle and apoptosis was minimum after such short repair intervals and the data, thus, reflect mainly the amount of dsb induced and initial repair efficiency.
To this end, we first tested the correlation of the expression values of several random combinations of minimum 4 genes, covering all phases of the cell cycle, with the original GGI.
We discovered that the potential landscape of yeast cell cycle network is funneled toward the global minimum, G1 state.
Microneme mRNA profiles in synchronized parasites are offset in time (1 2 h) from rhoptry mRNAs (compare Fig. 4E to G) with minimum levels in mid-to-late G1, clearly past the point of cell cycle arrest in mutant 88A5.
In addition, we have undertaken an unbiased re-evaluation of changes in gene expression across the cell cycle at a system-wide level, using an experimental strategy designed to cause minimum perturbation to the physiology of cell cycle progression in the cells being analyzed.
This gamete pedigree depth, achieved with a steep cell cycle gradient that is further discussed below, is substantially lower than the theoretical minimum of 11.55 for the production of 3000 cells.
