Clustering analysis of total and active RNAP II at genes during the transition from G1 to G2 [Dataset]

A) Overview of the different clusters identified through SOTA analysis. B) Behavior of total RNAP II (RNAp ChIP) and active RNAP II (GRO) in each identified cluster. mRNA expression and mRNA decay data from Eser et al. [17] are also presented. Genes included in each cluster, along with all transcriptomic data, are listed in S1 Table. To determine the proportion of active polymerases, we performed a linear regression analysis using GRO as the dependent variable and RNAp ChIP as the predictor, without an intercept term. The resulting regression coefficient represents the fraction of RNA polymerases actively engaged in transcription. By interpreting this coefficient as the efficiency of polymerase engagement, we estimate the percentage of active polymerases relative to the total chromatin-bound population. C) Distribution of cell cycle genes according to their peak of maximal expression (CellCycleBase 3.0) [18] in each of the clusters identified. Green arrows indicate groups in which the enrichment or depletion of cell cycle genes is statistically significant (logistic regression with Benjamini-Hochberg correction). D) Transcription factors known to regulate genes belonging to the clusters described in A. Only transcription factors significantly enriched in one or two clusters (Yeastrack [25], hypergeometric test p < 10 ⁻ ⁵), according to DNA binding or expression evidence, are shown. Other transcription factors significantly enriched in three or more clusters include: Bas1, Cst6, Tec1, Gat1, Cbf1, Met28, Pdr1, Gcn4, Met31, Met32, Pdr3, Rpn4, and Yap1.