(a) A schematic illustration of the telegraph model. (b). A schematic of the delay telegraph model. The double horizontal line for nascent mRNA removal indicates this is a delayed reaction. (c) …
(a) 3D scatter plot showing the ratio of the mean relative error from nascent mRNA data (using delay telegraph model ) and the mean relative error from mature mRNA data (using the telegraph model ) for 789 independent parameter sets sampled on a grid. Red data points indicate parameter sets with lower relative errors for mature data compared to nascent data, blue datapoints indicate parameter sets with lower relative error for nascent data compared to mature data (b) Same data as (a) but shown as a function of the fraction of ON time, . For of the parameters, the inference accuracy is higher when using nascent mRNA data. (c) Sampling from the same parameter space, we then add log-normal distributed noise (size 5%) to the initiation rate (see text for details) to mimic external noise due to post-transcriptional processing that is only present in mature mRNA. Log10 of the ratio of the median relative error (MRE) using perturbed mature mRNA data against Log10 MRE using nascent mRNA data is shown as a function of the true fraction of ON time, . For of the parameters, the inference accuracy is higher when using nascent mRNA data. (d) The median relative error of each transcriptional parameter as a function of the fraction of ON time, using synthetic nascent mRNA, synthetic mature mRNA data and synthetic mature mRNA with external noise. Inference from nascent data is generally more accurate than using mature mRNA data.
(a) Representative smFISH image of a yeast cell with PP7-GAL10 RNAs labeled with Cy3 and the nucleus labeled with DAPI. (b) The DAPI and Cy3 signals were used to determine the nuclear and cellular …
(a) Normalized nascent mRNA distributions of merged cell-cycle data were obtained by normalizing the signal intensity of the transcription site (defined as the brightest spot in the cell) by the …
(a) Nascent RNA distributions for cell-cycle-specific and merged data. Black lines represent best fits with delay telegraph model using the rejection method. (only the distributions for dataset #1 …
(a) Estimated burst size, fraction of ON and Fano factor (mean values and standard deviation error bars of the four datasets) by combining the first bins with . (b) Corresponding fitted …
(a) Ratio of the mean relative errors in the two types of data as a function of the true fraction of ON time, . For ≈91% (719/789) of the parameters, the inference accuracy is higher when using …
(a) Estimates using the inference algorithm with the telegraph model (with no external noise) for six parameter sets. For both the ground truth and the estimated parameters, we fix the degradation …
(a-d) Comparison of the stochastic properties of the delay telegraph model and the telegraph model. a. Distributions of the nascent mRNA predicted by the delay telegraph model and the telegraph …
(a) Merged mature mRNA count distribution (purple) under segmentation method 1 and with/without counting the transcriptional site (TS) under segmentation method 2 with a best fit obtained from the …
Experimental distributions (purple) are fit using the delay telegraph model (magenta curves).
Corresponding fitted distributions (purple) for G1 (top row) and G2 (bottom row) using the delay telegraph model (magenta curves).
The transcriptional parameters for G1 and G2 cells in the four sets of experimental data were obtained using the fusion method (see Figure 6d of the main manuscript). A linear fit (dashed black …
Right panel: These instabilities disappear when the precision increases to 300. The exact solution with such high precision agrees well with the FSP method using double-precision floating-point …
Magenta curves (Method 2) show the same but using a bimodal Gaussian, as described in the main text.
Parameter | Mean | Standard deviation | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
burst size | burst size | |||||||||
Set 1 | 31.85 | 2.69 | 15.68 | 0.53 | 0.10 | 19.07 | 0.22 | 7.68 | 0.07 | 0.05 |
Set 2 | 92.67 | 30.47 | 141.42 | 1.56 | 0.25 | 23.76 | 1.51 | 21.61 | 0.14 | 0.04 |
Set 3 | 9.94 | 8.01 | 63.35 | 6.39 | 0.45 | 0.72 | 0.19 | 1.94 | 0.25 | 0.01 |
Set 4 | 2.30 | 2.16 | 18.76 | 8.17 | 0.48 | 0.12 | 0.05 | 0.31 | 0.31 | 0.01 |
Set 5 | 2.26 | 5.80 | 12.57 | 5.59 | 0.72 | 0.19 | 0.30 | 0.11 | 0.41 | 0.01 |
Set 6 | 1.22 | 10.01 | 24.97 | 20.53 | 0.89 | 0.10 | 0.43 | 0.16 | 1.65 | 0.01 |
Parameter | Telegraph CI | Delay CI | ||||
---|---|---|---|---|---|---|
Set 1 | (6.76, 300.00) | (3.53, 8.49) | (5.59, 107.67) | (13.80, 300.00) | (1.85, 2.69) | (9.94, 160.51) |
Set 2 | (17.22, 190.38) | (14.56, 23.92) | (61.14, 250.51) | (103.80, 268.35) | (30.00, 35.38) | (161.54, 300.00) |
Set 3 | (0.54, 0.59) | (0.41, 0.43) | (46.08, 47.15) | (6.83, 8.55) | (6.42, 7.04) | (58.28, 63.18) |
Set 4 | (0.31, 0.35) | (0.46, 0.49) | (15.50, 15.91) | (1.64,1.99) | (1.65,1.85) | (17.92,18.77) |
Set 5 | (0.49, 0.85) | (5.82, 7.62) | (49.62, 50.92) | (1.56,2.59) | (4.58,5.85) | (12.08,12.97) |
Set 6 | (0.08, 0.16) | (2.46, 3.54) | (26.10, 26.54) | (0.73,1.24) | (7.53,9.75) | (24.32,25.14) |
See text for details.
Telegraph | Delay | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Relative error | Profile likelihood error | Relative error | Profile likelihood error | |||||||||
Set 1 | 0.87 | 0.27 | 0.77 | 18.82 | 0.88 | 11.07 | 0.82 | 0.11 | 0.58 | 1.75 | 0.34 | 1.82 |
Set 2 | 0.04 | 0.04 | 1.44E-03 | 4.72 | 0.52 | 2.22 | 0.41 | 0.11 | 0.27 | 0.81 | 0.16 | 0.55 |
Set 3 | 0.08 | 0.01 | 0.01 | 0.09 | 0.06 | 0.02 | 0.20 | 0.15 | 0.03 | 0.22 | 0.09 | 0.08 |
Set 4 | 0.01 | 0.01 | 1.11E-03 | 0.14 | 0.07 | 0.03 | 0.22 | 0.18 | 0.02 | 0.20 | 0.11 | 0.05 |
Set 5 | 0.22 | 0.13 | 4.97E-03 | 0.55 | 0.27 | 0.03 | 0.30 | 0.23 | 0.03 | 0.64 | 0.28 | 0.07 |
Set 6 | 0.29 | 0.24 | 0.01 | 0.74 | 0.37 | 0.02 | 0.20 | 0.12 | 0.01 | 0.55 | 0.25 | 0.03 |
Parameter | True | Unperturbed | –1/0/+1 stochastic perturbation | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
burst size | burst size | burst size | |||||||||||||
Set 1 | 120.38 | 7.70 | 40.85 | 0.34 | 0.06 | 15.58 | 5.63 | 9.22 | 0.59 | 0.27 | 0.59 | 1.17 | 3.70 | 6.28 | 0.66 |
Set 2 | 35.48 | 17.39 | 85.05 | 2.40 | 0.33 | 36.73 | 18.03 | 85.17 | 2.32 | 0.33 | 24.13 | 15.79 | 70.89 | 2.94 | 0.40 |
Set 3 | 0.52 | 0.42 | 46.21 | 88.36 | 0.44 | 0.57 | 0.42 | 46.62 | 82.47 | 0.43 | 0.61 | 0.46 | 47.17 | 76.74 | 0.43 |
Set 4 | 0.32 | 0.47 | 15.71 | 48.65 | 0.59 | 0.33 | 0.47 | 15.70 | 48.01 | 0.59 | 0.39 | 0.54 | 16.09 | 41.17 | 0.58 |
Set 5 | 0.53 | 5.85 | 49.95 | 94.72 | 0.92 | 0.64 | 6.62 | 50.20 | 77.99 | 0.91 | 0.68 | 6.72 | 50.35 | 74.48 | 0.91 |
Set 6 | 0.16 | 3.89 | 26.45 | 169.81 | 0.96 | 0.11 | 2.94 | 26.30 | 238.76 | 0.96 | 0.13 | 3.06 | 26.42 | 203.20 | 0.96 |
Parameter | True | Delay | Perturbation | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
burst size | burst size | burst size | |||||||||||||
Set 1 | 34.49 | 2.80 | 16.65 | 0.48 | 0.08 | 62.74 | 3.10 | 26.38 | 0.42 | 0.05 | 50.08 | 1.52 | 31.71 | 0.63 | 0.03 |
Set 2 | 135.68 | 32.98 | 179.74 | 1.32 | 0.20 | 80.42 | 29.44 | 131.35 | 1.63 | 0.27 | 233.96 | 30.74 | 300.00 | 1.28 | 0.12 |
Set 3 | 9.86 | 7.96 | 63.16 | 6.41 | 0.45 | 7.85 | 6.78 | 61.20 | 7.79 | 0.46 | 8.85 | 6.63 | 65.49 | 7.40 | 0.43 |
Set 4 | 2.26 | 2.14 | 18.64 | 8.26 | 0.49 | 1.77 | 1.76 | 18.28 | 10.36 | 0.50 | 1.90 | 1.64 | 18.65 | 9.83 | 0.46 |
Set 5 | 2.27 | 5.80 | 12.55 | 5.53 | 0.72 | 1.60 | 4.48 | 12.21 | 7.63 | 0.74 | 2.59 | 4.79 | 13.27 | 5.13 | 0.65 |
Set 6 | 1.18 | 9.94 | 24.92 | 21.15 | 0.89 | 0.94 | 8.74 | 24.74 | 26.37 | 0.90 | 1.84 | 10.15 | 26.10 | 14.18 | 0.85 |
Parameter | True | Delay | Telegraph | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
burst size | burst size | burst size | |||||||||||||
Set 1 | 1.05 | 8.20 | 57.99 | 55.09 | 0.89 | 0.94 | 7.19 | 57.92 | 61.87 | 0.88 | 0.60 | 4.10 | 59.51 | 99.42 | 0.87 |
Set 2 | 1.27 | 3.14 | 58.17 | 45.69 | 0.71 | 1.13 | 2.91 | 58.01 | 51.16 | 0.72 | 0.45 | 1.22 | 59.43 | 133.07 | 0.73 |
Set 3 | 2.27 | 5.80 | 12.55 | 5.53 | 0.72 | 1.60 | 4.48 | 12.21 | 7.63 | 0.74 | 0.59 | 1.71 | 12.09 | 20.61 | 0.74 |
Set 4 | 1.18 | 9.94 | 24.92 | 21.15 | 0.89 | 0.94 | 8.74 | 24.74 | 26.37 | 0.90 | 0.46 | 4.12 | 24.92 | 54.00 | 0.90 |
Set 5 | 2.26 | 2.14 | 18.64 | 8.26 | 0.49 | 1.77 | 1.76 | 18.28 | 10.36 | 0.50 | 0.54 | 0.58 | 17.60 | 32.59 | 0.52 |
Set 6 | 1.38 | 4.77 | 21.74 | 15.79 | 0.78 | 1.08 | 4.00 | 21.50 | 19.94 | 0.79 | 0.38 | 1.49 | 21.31 | 56.44 | 0.80 |
Parameter | segmentation 1 | segmentation 2 | segmentation 2 without TS | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
burst size | burst size | burst size | |||||||||||||
Set 1 | 21.18 | 4.73 | 47.15 | 2.23 | 0.18 | 3.27 | 3.36 | 20.62 | 6.31 | 0.51 | 2.92 | 2.45 | 21.05 | 7.22 | 0.46 |
Set 2 | 19.53 | 5.44 | 40.11 | 2.05 | 0.22 | 3.22 | 3.87 | 19.17 | 5.95 | 0.55 | 2.46 | 2.68 | 18.35 | 7.46 | 0.52 |
Set 3 | 16.53 | 4.77 | 39.48 | 2.39 | 0.22 | 3.67 | 4.05 | 20.09 | 5.47 | 0.52 | 3.00 | 2.87 | 19.73 | 6.57 | 0.49 |
Set 4 | 28.72 | 5.16 | 50.00 | 1.74 | 0.15 | 5.79 | 4.58 | 23.04 | 3.98 | 0.44 | 5.27 | 3.27 | 24.33 | 4.61 | 0.38 |
Mean | 21.49 | 5.02 | 44.19 | 2.10 | 0.19 | 3.99 | 3.97 | 20.73 | 5.43 | 0.50 | 3.41 | 2.82 | 20.87 | 6.46 | 0.46 |
Std | 5.19 | 0.34 | 5.21 | 0.28 | 0.03 | 1.06 | 0.43 | 1.43 | 0.89 | 0.04 | 1.26 | 0.35 | 2.56 | 1.29 | 0.06 |
mature | CI for | ||||||
---|---|---|---|---|---|---|---|
merged | Set 1 | 3.27 | 3.36 | 20.62 | (2.08, 6.08) | (2.81, 4.16) | (18.03, 25.97) |
Set 2 | 3.22 | 3.87 | 19.17 | (2.38, 4.69) | (3.41, 4.44) | (17.51, 21.62) | |
Set 3 | 3.67 | 4.05 | 20.09 | (2.54, 5.92) | (3.51, 4.79) | (18.03, 23.67) | |
Set 4 | 5.79 | 4.58 | 23.04 | (3.33, 13.33) | (3.79, 5.85) | (19.36, 33.51) | |
G1 | Set 1 | 0.69 | 2.76 | 10.71 | (0.27, 2.35) | (1.73, 4.96) | (9.77, 12.85) |
Set 2 | 0.60 | 2.80 | 10.27 | (0.35, 1.24) | (2.13, 3.92) | (9.77, 11.15) | |
Set 3 | 0.88 | 3.41 | 10.33 | (0.38, 2.84) | (2.23, 5.77) | (9.58, 12.35) | |
Set 4 | 2.46 | 5.21 | 11.12 | (0.46, 300.00) | (2.68, 18.86) | (8.96, 216.67) | |
G2 | Set 1 | 0.42 | 0.99 | 9.45 | (0.22, 0.91) | (0.65, 1.48) | (8.64, 10.86) |
Set 2 | 0.14 | 1.01 | 7.92 | (0.05, 0.36) | (0.56, 1.72) | (7.61, 8.46) | |
Set 3 | 0.18 | 1.24 | 7.91 | (0.05, 0.72) | (0.57, 2.59) | (7.49, 8.85) | |
Set 4 | 0.42 | 1.68 | 8.19 | (0.12, 2.07) | (0.76, 3.50) | (7.41, 10.28) |
mature | burst size | |||||
---|---|---|---|---|---|---|
G2 sync | Set 1 | 0.62 | 2.17 | 8.45 | 13.69 | 0.78 |
Set 2 | 0.37 | 3.26 | 7.72 | 21.05 | 0.90 | |
Set 3 | 0.67 | 4.42 | 7.92 | 11.85 | 0.87 | |
Set 4 | 0.55 | 3.45 | 7.55 | 13.62 | 0.86 | |
Mean | 0.55 | 3.32 | 7.91 | 15.05 | 0.85 | |
Std | 0.13 | 0.92 | 0.39 | 4.09 | 0.05 |
The elongation time is estimated to be 0.785 min, based on measurements of the elongation speed.
nascent | burst size | |||||
---|---|---|---|---|---|---|
merged | Set 1 | 5.24 | 5.07 | 77.46 | 14.78 | 0.49 |
Set 2 | 5.58 | 5.13 | 82.11 | 14.71 | 0.48 | |
Set 3 | 5.11 | 5.17 | 76.09 | 14.90 | 0.50 | |
Set 4 | 5.96 | 6.13 | 73.23 | 12.30 | 0.51 | |
Mean | 5.47 | 5.37 | 77.22 | 14.17 | 0.50 | |
Std | 0.38 | 0.50 | 3.70 | 1.25 | 0.01 | |
G1 | Set 1 | 1.11 | 3.76 | 37.83 | 34.10 | 0.77 |
Set 2 | 1.53 | 3.94 | 41.33 | 27.06 | 0.72 | |
Set 3 | 0.95 | 3.23 | 36.79 | 38.56 | 0.77 | |
Set 4 | 1.28 | 3.76 | 36.04 | 28.09 | 0.75 | |
Mean | 1.22 | 3.67 | 38.00 | 31.95 | 0.75 | |
Std | 0.25 | 0.31 | 2.34 | 5.39 | 0.02 | |
G2 | Set 1 | 0.74 | 1.69 | 35.00 | 47.30 | 0.70 |
Set 2 | 0.82 | 2.18 | 36.30 | 44.37 | 0.73 | |
Set 3 | 0.91 | 2.19 | 34.54 | 37.90 | 0.71 | |
Set 4 | 1.08 | 2.61 | 33.27 | 30.76 | 0.71 | |
Mean | 0.89 | 2.17 | 34.78 | 40.08 | 0.71 | |
Std | 0.15 | 0.38 | 1.25 | 7.35 | 0.01 |
nascent | burst size | CI for | |||||||
---|---|---|---|---|---|---|---|---|---|
merged | Set 1 | 5.24 | 5.07 | 77.46 | 14.78 | 0.49 | (4.42, 6.23) | (4.68, 5.45) | (73.48, 82.92) |
Set 2 | 5.58 | 5.13 | 82.11 | 14.71 | 0.48 | (5.05, 6.15) | (4.97, 5.37) | (79.38, 85.53) | |
Set 3 | 5.11 | 5.17 | 76.09 | 14.90 | 0.50 | (4.53, 5.71) | (4.98, 5.38) | (73.49, 79.64) | |
Set 4 | 5.96 | 6.13 | 73.23 | 12.30 | 0.51 | (5.19, 7.22) | (5.87, 6.57) | (69.34, 78.37) | |
G1 | Set 1 | 1.11 | 3.76 | 37.83 | 34.10 | 0.77 | (0.77, 1.66) | (3.04, 4.63) | (36.26, 39.96) |
Set 2 | 1.53 | 3.94 | 41.33 | 27.06 | 0.72 | (1.29, 1.88) | (3.64, 4.40) | (40.18, 42.85) | |
Set 3 | 0.95 | 3.23 | 36.79 | 38.56 | 0.77 | (0.77, 1.17) | (2.86, 3.60) | (36.05, 37.69) | |
Set 4 | 1.28 | 3.76 | 36.04 | 28.09 | 0.75 | (0.99, 1.73) | (3.18, 4.34) | (34.68, 37.75) | |
G2 | Set 1 | 0.74 | 1.69 | 35.00 | 47.30 | 0.70 | (0.54, 1.02) | (1.36, 2.08) | (33.64, 36.72) |
Set 2 | 0.82 | 2.18 | 36.30 | 44.37 | 0.73 | (0.66, 1.07) | (1.85, 2.52) | (35.35, 37.40) | |
Set 3 | 0.91 | 2.19 | 34.54 | 37.90 | 0.71 | (0.70, 1.23) | (1.85, 2.61) | (33.38, 36.05) | |
Set 4 | 1.08 | 2.61 | 33.27 | 30.76 | 0.71 | (0.75, 1.71) | (2.00, 3.41) | (31.91, 35.40) |
Inference is done for each of the four data sets. The elongation time is fixed to min.
k = 1 | burst size | |||||
---|---|---|---|---|---|---|
G1 | Set 1 | 1.06 | 4.33 | 36.62 | 34.63 | 0.80 |
Set 2 | 1.45 | 4.42 | 39.84 | 27.51 | 0.75 | |
Set 3 | 1.04 | 3.84 | 36.66 | 35.19 | 0.79 | |
Set 4 | 1.27 | 4.12 | 35.41 | 27.78 | 0.76 | |
Mean | 1.21 | 4.18 | 37.13 | 31.28 | 0.78 | |
Std | 0.19 | 0.26 | 1.90 | 4.20 | 0.02 | |
G2 | Set 1 | 0.84 | 2.10 | 34.54 | 41.20 | 0.71 |
Set 2 | 0.97 | 2.94 | 35.49 | 36.73 | 0.75 | |
Set 3 | 0.94 | 2.53 | 33.68 | 35.99 | 0.73 | |
Set 4 | 1.20 | 3.07 | 32.81 | 27.28 | 0.72 | |
Mean | 0.99 | 2.66 | 34.13 | 35.30 | 0.73 | |
Std | 0.15 | 0.44 | 1.15 | 5.82 | 0.02 | |
burst size | ||||||
G1 | Set 1 | 1.58 | 6.33 | 37.77 | 23.89 | 0.80 |
Set 2 | 1.93 | 5.93 | 40.86 | 21.16 | 0.75 | |
Set 3 | 1.28 | 5.15 | 37.07 | 29.07 | 0.80 | |
Set 4 | 1.55 | 5.29 | 35.92 | 23.10 | 0.77 | |
Mean | 1.59 | 5.67 | 37.91 | 24.30 | 0.78 | |
Std | 0.27 | 0.55 | 2.11 | 3.38 | 0.02 | |
G2 | Set 1 | 1.43 | 3.42 | 35.83 | 25.11 | 0.71 |
Set 2 | 1.69 | 4.39 | 37.42 | 22.10 | 0.72 | |
Set 3 | 1.33 | 3.38 | 34.64 | 26.08 | 0.72 | |
Set 4 | 1.56 | 3.68 | 33.70 | 21.61 | 0.70 | |
Mean | 1.50 | 3.72 | 35.39 | 23.72 | 0.71 | |
Std | 0.16 | 0.47 | 1.61 | 2.20 | 0.01 | |
burst size | ||||||
G1 | Set 1 | 2.66 | 9.03 | 39.73 | 14.92 | 0.77 |
Set 2 | 2.55 | 7.41 | 42.04 | 16.46 | 0.74 | |
Set 3 | 1.64 | 6.67 | 37.69 | 22.92 | 0.80 | |
Set 4 | 2.22 | 7.32 | 37.02 | 16.65 | 0.77 | |
Mean | 2.27 | 7.61 | 39.12 | 17.73 | 0.77 | |
Std | 0.46 | 1.00 | 2.26 | 3.54 | 0.02 | |
G2 | Set 1 | 2.01 | 4.35 | 37.23 | 18.50 | 0.68 |
Set 2 | 2.16 | 5.10 | 38.56 | 17.85 | 0.70 | |
Set 3 | 1.70 | 4.05 | 35.55 | 20.85 | 0.70 | |
Set 4 | 1.88 | 4.16 | 34.48 | 18.30 | 0.69 | |
Mean | 1.94 | 4.41 | 36.45 | 18.88 | 0.69 | |
Std | 0.19 | 0.48 | 1.80 | 1.34 | 0.01 | |
burst size | ||||||
G1 | Set 1 | 6.10 | 14.18 | 44.41 | 7.28 | 0.70 |
Set 2 | 3.72 | 9.57 | 43.96 | 11.81 | 0.72 | |
Set 3 | 2.02 | 7.99 | 38.25 | 18.89 | 0.80 | |
Set 4 | 2.75 | 8.60 | 37.78 | 13.76 | 0.76 | |
Mean | 3.65 | 10.09 | 41.10 | 12.94 | 0.74 | |
Std | 1.77 | 2.80 | 3.57 | 4.81 | 0.04 | |
G2 | Set 1 | 2.12 | 4.50 | 37.48 | 17.68 | 0.68 |
Set 2 | 2.59 | 5.68 | 39.55 | 15.25 | 0.69 | |
Set 3 | 2.47 | 5.14 | 37.27 | 15.08 | 0.68 | |
Set 4 | 2.18 | 4.55 | 35.17 | 16.13 | 0.68 | |
Mean | 2.34 | 4.97 | 37.37 | 16.04 | 0.68 | |
Std | 0.23 | 0.56 | 1.79 | 1.19 | 0.01 |
Inference is done for each of the four data sets. The elongation time is fixed to min.
burst size | ||||||
---|---|---|---|---|---|---|
G1 | Set 1 | 1.11 | 3.76 | 37.83 | 34.10 | 0.77 |
Set 2 | 1.53 | 3.94 | 41.33 | 27.06 | 0.72 | |
Set 3 | 0.95 | 3.23 | 36.79 | 38.56 | 0.77 | |
Set 4 | 1.28 | 3.76 | 36.04 | 28.09 | 0.75 | |
Mean | 1.22 | 3.67 | 38.00 | 31.95 | 0.75 | |
Std | 0.25 | 0.31 | 2.34 | 5.39 | 0.02 | |
G2 | Set 1 | 0.74 | 1.69 | 35.00 | 47.30 | 0.70 |
Set 2 | 0.82 | 2.18 | 36.30 | 44.37 | 0.73 | |
Set 3 | 0.91 | 2.19 | 34.54 | 37.90 | 0.71 | |
Set 4 | 1.08 | 2.61 | 33.27 | 30.76 | 0.71 | |
Mean | 0.89 | 2.17 | 34.78 | 40.08 | 0.71 | |
Std | 0.15 | 0.38 | 1.25 | 7.35 | 0.01 | |
burst size | ||||||
G1 | Set 1 | 0.78 | 2.99 | 36.65 | 46.99 | 0.79 |
Set 2 | 1.14 | 3.27 | 40.01 | 35.06 | 0.74 | |
Set 3 | 0.71 | 2.58 | 36.00 | 51.00 | 0.79 | |
Set 4 | 0.96 | 3.09 | 35.08 | 36.52 | 0.76 | |
Mean | 0.90 | 2.98 | 36.94 | 42.39 | 0.77 | |
Std | 0.19 | 0.30 | 2.15 | 7.82 | 0.02 | |
G2 | Set 1 | 0.54 | 1.30 | 34.37 | 63.20 | 0.70 |
Set 2 | 0.67 | 1.87 | 35.74 | 53.70 | 0.74 | |
Set 3 | 0.74 | 1.88 | 33.96 | 45.75 | 0.72 | |
Set 4 | 0.94 | 2.36 | 32.84 | 34.89 | 0.72 | |
Mean | 0.72 | 1.85 | 34.23 | 49.38 | 0.72 | |
Std | 0.17 | 0.44 | 1.20 | 12.01 | 0.01 | |
burst size | ||||||
G1 | Set 1 | 0.71 | 2.79 | 36.38 | 51.39 | 0.80 |
Set 2 | 1.07 | 3.14 | 39.77 | 37.01 | 0.75 | |
Set 3 | 0.63 | 2.35 | 35.74 | 56.84 | 0.79 | |
Set 4 | 0.80 | 2.71 | 34.58 | 43.09 | 0.77 | |
Mean | 0.80 | 2.75 | 36.62 | 47.08 | 0.78 | |
Std | 0.19 | 0.32 | 2.23 | 8.78 | 0.02 | |
G2 | Set 1 | 0.52 | 1.25 | 34.30 | 65.86 | 0.71 |
Set 2 | 0.65 | 1.84 | 35.70 | 54.75 | 0.74 | |
Set 3 | 0.71 | 1.81 | 33.85 | 47.67 | 0.72 | |
Set 4 | 0.91 | 2.31 | 32.76 | 35.91 | 0.72 | |
Mean | 0.70 | 1.80 | 34.15 | 51.05 | 0.72 | |
Std | 0.16 | 0.43 | 1.22 | 12.57 | 0.01 | |
burst size | ||||||
G1 | Set 1 | 0.69 | 2.73 | 36.30 | 52.85 | 0.80 |
Set 2 | 1.05 | 3.09 | 39.69 | 37.71 | 0.75 | |
Set 3 | 0.63 | 2.35 | 35.74 | 56.78 | 0.79 | |
Set 4 | 0.83 | 2.79 | 34.68 | 41.57 | 0.77 | |
Mean | 0.80 | 2.74 | 36.60 | 47.23 | 0.78 | |
Std | 0.19 | 0.31 | 2.17 | 9.04 | 0.02 | |
G2 | Set 1 | 0.56 | 1.34 | 34.45 | 61.05 | 0.70 |
Set 2 | 0.66 | 1.86 | 35.73 | 54.11 | 0.74 | |
Set 3 | 0.67 | 1.72 | 33.70 | 50.56 | 0.72 | |
Set 4 | 0.92 | 2.33 | 32.79 | 35.48 | 0.72 | |
Mean | 0.70 | 1.81 | 34.17 | 50.30 | 0.72 | |
Std | 0.15 | 0.41 | 1.24 | 10.80 | 0.01 |
Inferred values and the corresponding 95% confidence intervals of G1 and G2 cell-cycle-specific data calculated using the profile likelihood method.
nascent | burst size | CI for | |||||||
---|---|---|---|---|---|---|---|---|---|
G1 | Set 1 | 0.69 | 2.73 | 36.30 | 52.85 | 0.80 | (0.46, 1.05) | (2.12, 3.52) | (35.06, 37.91) |
Set 2 | 1.05 | 3.09 | 39.69 | 37.71 | 0.75 | (0.86, 1.29) | (2.73, 3.47) | (38.77, 40.92) | |
Set 3 | 0.63 | 2.35 | 35.74 | 56.78 | 0.79 | (0.49, 0.79) | (1.99, 2.71) | (35.06, 36.58) | |
Set 4 | 0.83 | 2.79 | 34.68 | 41.57 | 0.77 | (0.62, 1.16) | (2.27, 3.41) | (33.54, 36.01) | |
G2 | Set 1 | 0.56 | 1.34 | 34.45 | 61.05 | 0.70 | (0.40, 0.81) | (1.04, 1.73) | (33.35, 35.82) |
Set 2 | 0.66 | 1.86 | 35.73 | 54.11 | 0.74 | (0.51, 0.85) | (1.57, 2.21) | (34.87, 36.77) | |
Set 3 | 0.67 | 1.72 | 33.70 | 50.56 | 0.72 | (0.50, 0.91) | (1.40, 2.11) | (32.78, 34.87) | |
Set 4 | 0.92 | 2.33 | 32.79 | 35.48 | 0.72 | (0.62, 1.45) | (1.74, 3.09) | (31.65, 34.68) |
nascent fusion | burst size | |||||
---|---|---|---|---|---|---|
G2 sync | Set 1 | 1.84 | 4.42 | 33.84 | 18.42 | 0.71 |
Set 2 | 2.18 | 5.78 | 35.85 | 16.44 | 0.73 | |
Set 3 | 2.15 | 5.36 | 33.61 | 15.63 | 0.71 | |
Set 4 | 3.53 | 7.45 | 34.16 | 9.69 | 0.68 | |
Mean | 2.42 | 5.75 | 34.36 | 15.05 | 0.71 | |
Std. | 0.75 | 1.26 | 1.01 | 3.76 | 0.02 |
Parameters same as in Appendix 6—figure 1. The time was calculated using the Julia package BenchmarkTools.jl.
Exact solution: precision = 85 | Exact solution: precision = 300 | FSP method | |
---|---|---|---|
Minimum time: | 6.422ms | 9.277ms | 8.317ms |
Median time: | 6.868ms | 9.562ms | 9.092ms |
Mean time: | 8.279ms | 11.482ms | 9.415ms |
Maximum time: | 16.791ms | 16.919ms | 14.203ms |
# of Simulations: | 604 | 436 | 531 |