Fig. 5: Co-regulated clusters of TGFβ-regulated genes.

a, b Examples of clusters of TGFβ co-regulated genes. Screenshot of RNA-seq tracks at two different genomic regions. Numbers show Log₂FC of the indicated gene at the corresponding timepoint of TGFβ versus vehicle. c Changes of mRNA levels (RNA-seq) of the four genes located upstream (n − 1 to n − 4) and downstream (n + 1 to n + 4) of a robustly TGFβ-regulated gene (|log₂FC | >1; adjusted p < 0.05) at position n. The central gene (n) is early-upregulated (left) or early-downregulated (right). Gray boxes correspond to the changes of mRNA levels of genes around a random gene. For randomization, see Methods. d Change of mRNA levels (RNA-seq) of genes located at the indicated distance (kb) upstream or downstream of a TGFβ-regulated gene. Left: the central gene is early-upregulated. Right: the central gene is early-downregulated. Randomizations are shown in Supplementary Fig. 10d. c, d Statistical significance between real and random distributions were determined with the two-tailed Mann–Whitney non-parametric test, *p ≤ 0.05; **p ≤ 0.01; ***p ≤ 0.001. Sample size (n) of each distribution and exact p-values are provided in Supplementary Data 5. The horizontal black line of the boxplot represents the median value, the box spans the 25th to 75th percentiles, and whiskers indicate 5th and 95th percentiles. A black dot in the boxplot represent the mean. e Changes of intergenic transcription in the neighborhood (±250 kb binned in 10 kb bins) of a TGFβ-regulated gene (TRG) normalized to random. ChromRNA-seq data were used. To avoid termination read-through and promoter-divergent transcription, regions of 2 kb upstream and downstream of the TSS and transcription termination site were not considered. f Change of H3K27ac (ChIP-seq signal) in the neighborhood (±250 kb binned in 10 kb bins) of a TGFβ-regulated TSS normalized to random. To avoid histone modifications of the TGFβ-regulated TSS, regions of 5 kb upstream and downstream of the TSS were not considered. c–f Late-upregulated and late-downregulated categories are shown in Supplementary Fig. 10b, c, e, f. g Meta-analysis of TRDs. Density plots of changes of mRNA, eRNA, and H3K27ac levels are shown. Data from early- and late-upregulated or downregulated TRDs were pooled. Source data are provided as a Source Data file.