Exact(41)
The manual adjustments consisted of separating YHB1 from the Fzf1p response cluster and forming a separate cluster containing only YHB1.
For example, the genes in the Fzf1p response cluster (except YHB1) were up-regulated in E2 and down-regulated in E3 (Figure 3a wt vs. 3b wt).
After obtaining the new data of experiment E3, we realized the crucial separation within the Fzf1p response cluster was that between YHB1 and the rest of the cluster.
The energy cluster included genes in the previously designated oxidative phosphorylation cluster and genes in the glucose utilization pathway that were previously in the galactose response cluster.
Only one cluster (the "extracellular matrix-immune response cluster") cannot be separated by edge-betweenness clustering at the point of maximal graph modularity.
Immune response cluster genes were reported as differentially regulated in inflammatory conditions such as ulcerative colitis, Crohn's disease, and Helicobacter pylori infections.
Similar(19)
Use of the linear mixed-effects model described in Model 5 permitted the estimation of a mean response (population-specific) or a calibrated response (cluster-specific) for a new tree (Verbeke and Molenberghs [2000]).
In addition, the identification of response clusters, within which the responses might be considered continuous, enables the use of traditional response surface approximation for optimization.
Therefore, the Fzf1p response clusters were not separated into early and late response clusters as in the initial model.
To identify putative regulatory networks within the antioxidant response, clustering methods were used to partition the data according to RNA expression patterns through time.
Five major gene clusters were identified using correlation cutoff 0.75 with subsequent manual adjustment: Fzf1p early response, Fzf1p late response, ESR, oxidative phosphorylation, and galactose response clusters (Table 1).
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