J.M. Valverde & G. Dubra
This repository provides the source code and data for all the analyses performed in R for the publication “A Cyclin-dependent kinase-mediated phosphorylation switch of disordered protein condensation” (Valverde, Dubra et al., 2023). This current GitHub readme file was automatically generated, using R Studio, from an R markdown (README.Rmd) where all the code used in the paper is recompiled.
##
## Wilcoxon signed rank test with continuity correction
##
## data: psites_diso by variable
## V = 206396, p-value < 2.2e-16
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## -1.211715 -1.052488
## sample estimates:
## (pseudo)median
## -1.131956
##
## Wilcoxon signed rank test with continuity correction
##
## data: psites_diso by variable
## V = 22188, p-value < 2.2e-16
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## -1.890087 -1.491565
## sample estimates:
## (pseudo)median
## -1.679388
##
## Wilcoxon signed rank test with continuity correction
##
## data: psites_diso by variable
## V = 1340, p-value = 1.019e-14
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## -2.734868 -1.577823
## sample estimates:
## (pseudo)median
## -2.131005
##
## Wilcoxon rank sum test with continuity correction
##
## data: Percentage of disorder by target
## W = 167690, p-value < 2.2e-16
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## 21.63845 31.47638
## sample estimates:
## difference in location
## 26.64479
##
## Wilcoxon rank sum test with continuity correction
##
## data: Percentage of disorder by target
## W = 166252, p-value < 2.2e-16
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## 23.21311 34.28578
## sample estimates:
## difference in location
## 28.64125
##
## Wilcoxon rank sum test with continuity correction
##
## data: Percentage of disorder by target
## W = 165710, p-value < 2.2e-16
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## 20.31818 30.31861
## sample estimates:
## difference in location
## 25.25882
##
## Wilcoxon rank sum test with continuity correction
##
## data: Percentage of disorder by target
## W = 7707108, p-value < 2.2e-16
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## 18.79420 22.82949
## sample estimates:
## difference in location
## 20.8597
##
## Wilcoxon rank sum test with continuity correction
##
## data: Percentage of disorder by target
## W = 7269014, p-value < 2.2e-16
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## 16.62156 21.14240
## sample estimates:
## difference in location
## 18.87039
##
## Wilcoxon rank sum test with continuity correction
##
## data: Percentage of disorder by target
## W = 7348738, p-value < 2.2e-16
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## 16.82185 21.06136
## sample estimates:
## difference in location
## 18.95022
##
## Wilcoxon rank sum test with continuity correction
##
## data: Percentage of disorder by ANOVA
## W = 307032, p-value = 2.358e-13
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## -10.849034 -6.152332
## sample estimates:
## difference in location
## -8.45844
##
## Wilcoxon rank sum test with continuity correction
##
## data: Percentage of disorder by ANOVA
## W = 278128, p-value = 4.832e-13
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## -12.27983 -7.01995
## sample estimates:
## difference in location
## -9.613807
##
## Wilcoxon rank sum test with continuity correction
##
## data: Percentage of disorder by ANOVA
## W = 319366, p-value = 5.781e-10
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## -10.862103 -5.641645
## sample estimates:
## difference in location
## -8.265359
## subset n mean sd min Q1 median Q3 max
## 1 Phosphoproteome 15329 22.767 24.195 0.000 3.333 13.687 36.158 100.000
## 2 CDK 656 43.040 25.881 0.000 24.184 40.389 61.776 100.000
## 3 MAPK 408 36.539 25.173 0.000 15.237 31.296 53.273 98.487
## 4 AURK 412 44.438 24.141 0.291 27.811 40.845 60.857 100.000
## 5 PLK 459 39.847 25.215 0.000 18.771 38.403 57.566 100.000
## 6 NEK 43 28.806 22.094 2.448 10.339 25.741 43.054 85.624
## 7 DYRK 42 41.869 25.545 0.239 22.507 40.408 59.029 95.763
## percZero
## 1 9.485
## 2 0.762
## 3 1.225
## 4 0.000
## 5 0.654
## 6 0.000
## 7 0.000
##
## Kruskal-Wallis rank sum test
##
## data: Percentage of disorder by subset
## Kruskal-Wallis chi-squared = 1064.1, df = 6, p-value < 2.2e-16
## subset n nvalid mean sd min Q1 median Q3 max
## 1 Phosphoproteome 15329 15300 30.599 28.045 0.000 8.231 20.914 45.864 100.000
## 2 CDK 656 656 48.864 28.506 0.000 26.305 46.592 70.344 100.000
## 3 MAPK 408 408 41.036 28.074 0.000 15.497 35.394 61.269 100.000
## 4 AURK 412 412 50.031 27.638 0.000 28.291 44.873 72.685 100.000
## 5 PLK 459 459 46.872 29.169 0.346 21.257 45.455 69.699 100.000
## 6 NEK 43 43 33.073 26.195 0.000 10.570 30.476 50.330 100.000
## 7 DYRK 42 42 46.485 26.216 6.310 25.558 45.340 61.612 99.548
## percZero
## 1 0.791
## 2 0.457
## 3 0.245
## 4 0.243
## 5 0.000
## 6 2.326
## 7 0.000
##
## Kruskal-Wallis rank sum test
##
## data: Percentage of disorder by subset
## Kruskal-Wallis chi-squared = 680.57, df = 6, p-value < 2.2e-16
## subset n nvalid mean sd min Q1 median Q3
## 1 Phosphoproteome 15329 15309 43.241 25.440 1.980 21.942 37.717 62.359
## 2 CDK 656 656 61.190 23.712 10.583 43.233 61.230 80.563
## 3 MAPK 408 408 54.506 23.997 7.042 33.354 54.216 76.560
## 4 AURK 412 412 62.686 21.933 10.738 45.588 62.748 80.284
## 5 PLK 459 459 59.330 24.128 10.406 38.498 60.535 79.393
## 6 NEK 43 43 49.955 22.278 14.161 29.756 52.847 63.672
## 7 DYRK 42 42 59.229 24.553 19.616 40.189 59.548 74.960
## max
## 1 100.000
## 2 100.000
## 3 100.000
## 4 100.000
## 5 100.000
## 6 95.455
## 7 100.000
##
## Kruskal-Wallis rank sum test
##
## data: Percentage of disorder by subset
## Kruskal-Wallis chi-squared = 751.44, df = 6, p-value < 2.2e-16
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##
## Wilcoxon rank sum test with continuity correction
##
## data: thalf by group
## W = 18.5, p-value = 0.1232
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## -13.370047 1.150055
## sample estimates:
## difference in location
## -4.977137
##
## Wilcoxon rank sum test with continuity correction
##
## data: thalf by group
## W = 0, p-value = 0.01421
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## -23.110004 -6.819955
## sample estimates:
## difference in location
## -15.94311
##
## Wilcoxon rank sum test with continuity correction
##
## data: thalf by group
## W = 15, p-value = 0.008276
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## -15.209962 -5.260037
## sample estimates:
## difference in location
## -11.23145
##
## Wilcoxon rank sum test with continuity correction
##
## data: percent by group
## W = 73, p-value = 0.005126
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## 11.17000 45.76001
## sample estimates:
## difference in location
## 27.58075
##
## Wilcoxon rank sum test with continuity correction
##
## data: percent by group
## W = 24, p-value = 0.01421
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## 17.58995 51.27007
## sample estimates:
## difference in location
## 30.0655
##
## Wilcoxon rank sum test with continuity correction
##
## data: percent by group
## W = 66, p-value = 0.5885
## alternative hypothesis: true location shift is not equal to 0
## 95 percent confidence interval:
## -10.63997 17.64000
## sample estimates:
## difference in location
## 2.790034
##
## Kruskal-Wallis rank sum test
##
## data: Foci_Nucleus by Treat_collapsed
## Kruskal-Wallis chi-squared = 205.15, df = 5, p-value < 2.2e-16
##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: Full_length_quant$Foci_Nucleus and Full_length_quant$Treat_collapsed
##
## DMSO L- DMSO L+ OA L- OA L+ PA L-
## DMSO L+ 2.1e-14 - - - -
## OA L- 5.3e-11 0.0230 - - -
## OA L+ 8.6e-14 0.3149 0.1860 - -
## PA L- 7.0e-05 < 2e-16 < 2e-16 < 2e-16 -
## PA L+ 0.6424 2.0e-15 1.8e-11 2.1e-14 0.0011
##
## P value adjustment method: BH
This block compares the residues predicted as to be disordered across the entire proteomes of yeast and human using different disorders. A Venn diagram is generated to illustrate the overlap between different methods
Calculate the porcentage of disorder of yeast and human CDK targets vs the rest of the phosphoproteome with all available predictors
##
## Kruskal-Wallis rank sum test
##
## data: Foci_Nucleus by Treat_collapsed
## Kruskal-Wallis chi-squared = 204.5, df = 5, p-value < 2.2e-16
##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: dLR_quant$Foci_Nucleus and dLR_quant$Treat_collapsed
##
## DMSO L- DMSO L+ OA L- OA L+ PA L-
## DMSO L+ < 2e-16 - - - -
## OA L- 2.3e-05 1.5e-10 - - -
## OA L+ < 2e-16 0.8143 2.9e-09 - -
## PA L- 0.7618 < 2e-16 2.9e-05 < 2e-16 -
## PA L+ 0.3916 < 2e-16 0.0014 8.9e-16 0.5839
##
## P value adjustment method: BH
##
## Kruskal-Wallis rank sum test
##
## data: Foci_Nucleus by Treat_collapsed
## Kruskal-Wallis chi-squared = 147.74, df = 5, p-value < 2.2e-16
##
## Pairwise comparisons using Wilcoxon rank sum test with continuity correction
##
## data: Repeats_LR_quant$Foci_Nucleus and Repeats_LR_quant$Treat_collapsed
##
## DMSO L- DMSO L+ OA L- OA L+ PA L-
## DMSO L+ 8.0e-09 - - - -
## OA L- 0.032 4.4e-05 - - -
## OA L+ 1.4e-09 0.341 3.3e-06 - -
## PA L- 3.3e-06 < 2e-16 3.0e-11 < 2e-16 -
## PA L+ 0.776 1.4e-09 0.014 2.8e-10 7.7e-06
##
## P value adjustment method: BH
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