Extended Data Fig. 3: Phenomenological two-state model fitting and robustness analysis.
From: Nonlinear control of transcription through enhancer–promoter interactions
a. Parameter values and 95% confidence intervals for the best fitting phenomenological two-state model. The rates are in the unit of RNA decay rate (\(\delta \)). b. Profile likelihood functions for all the parameters of the phenomenological two-state model. The red dashed line shows the threshold used to calculate the 95% confidence intervals (see Supplementary Model description for more details). c. Best fit of the phenomenological two-state model under different perturbations of the contact probabilities. Panels with blue curves show the best fit transcriptional responses when the scaling exponent of the contact probabilities was artificially set to 0.4, 0.5, 0.6, 0.7, 0.8, and 0.9. The scaling exponent of the original contact probabilities is 0.77. Panels with orange curves show the best fit transcriptional responses when contact probabilities were artificially increased by a factor 1/x with x = 0.1,...,0.9 with step of 0.1. Data are presented as average eGFP values calculated within equally spaced 20 kb bins +/- standard deviation (n = number of cell lines per bin), as in Fig. 1h. d. Left: Normalized mean eGFP intensities in individual eGFP+ cell lines are plotted as a function of the genomic position of the SCR. Data from 135 individual cell lines (light red dots) are presented as mean +/- standard deviation (n = 3 measurements performed on different days, as in panel g). Shaded grey area indicates the genomic regions that were excluded from the fit shown in the right panel. Right: Best fit of the phenomenological two-state model in the absence of the promoter-only control cell line and the cell lines with insertions that landed beyond the first CTCF site at the 3′ of the TAD (region highlighted in the left panel). Data are presented as average eGFP values calculated within equally spaced 20 kb bins +/- standard deviation (n = number of cell lines per bin). e. Profile likelihood function for the Hill coefficient for the fit described in panel d.
