search_index.json

[["hptm-transcription-dynamics.html", "S6 HPTM-transcription dynamics 6.1 H3K27me3 6.2 H3K27ac 6.3 H3K4me3 6.4 Comparison to random peaks", " S6 HPTM-transcription dynamics 6.1 H3K27me3 6.1.1 Gene bodies ## ## Call: ## glm(formula = H3K27me3_GB ~ Transcription + Group, family = "binomial", ## data = corrdat, na.action = na.exclude) ## ## Coefficients: ## Estimate Std. Error z value Pr(>|z|) ## (Intercept) 0.23128 0.01836 12.600 <2e-16 *** ## Transcription 1.52362 0.94428 1.614 0.107 ## Groupb1W -0.48789 0.02589 -18.843 <2e-16 *** ## Groupb2Q -0.46453 0.02586 -17.960 <2e-16 *** ## Groupb2W -0.53712 0.02593 -20.717 <2e-16 *** ## --- ## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 ## ## (Dispersion parameter for binomial family taken to be 1) ## ## Null deviance: 66993 on 48491 degrees of freedom ## Residual deviance: 66423 on 48487 degrees of freedom ## AIC: 66433 ## ## Number of Fisher Scoring iterations: 3 ## OR 2.5 % 97.5 % ## (Intercept) 1.2602085 1.2157024 1.3064034 ## Transcription 4.5887869 0.8272917 37.1403134 ## Groupb1W 0.6139213 0.5835273 0.6458649 ## Groupb2Q 0.6284311 0.5973523 0.6610940 ## Groupb2W 0.5844272 0.5554545 0.6148758 6.1.2 Promoters ## ## Call: ## glm(formula = H3K27me3_P ~ Transcription + Group, family = "binomial", ## data = corrdat, na.action = na.exclude) ## ## Coefficients: ## Estimate Std. Error z value Pr(>|z|) ## (Intercept) -0.19269 0.01842 -10.462 <2e-16 *** ## Transcription -3.50202 1.53037 -2.288 0.0221 * ## Groupb1W -0.43184 0.02643 -16.341 <2e-16 *** ## Groupb2Q -0.37462 0.02629 -14.249 <2e-16 *** ## Groupb2W -0.43267 0.02641 -16.384 <2e-16 *** ## --- ## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 ## ## (Dispersion parameter for binomial family taken to be 1) ## ## Null deviance: 64247 on 48491 degrees of freedom ## Residual deviance: 63863 on 48487 degrees of freedom ## AIC: 63873 ## ## Number of Fisher Scoring iterations: 4 ## OR 2.5 % 97.5 % ## (Intercept) 0.82474140 0.795490181 0.8550473 ## Transcription 0.03013634 0.001127849 0.4054232 ## Groupb1W 0.64931347 0.616521187 0.6838123 ## Groupb2Q 0.68755015 0.653001844 0.7238930 ## Groupb2W 0.64877540 0.616032490 0.6832215 6.2 H3K27ac 6.2.1 Gene bodies ## ## Call: ## glm(formula = H3K27ac_GB ~ Transcription + Group, family = "binomial", ## data = corrdat, na.action = na.exclude) ## ## Coefficients: ## Estimate Std. Error z value Pr(>|z|) ## (Intercept) 0.26665 0.01852 14.400 < 2e-16 *** ## Transcription 5.86657 1.65313 3.549 0.000387 *** ## Groupb1W -0.22906 0.02585 -8.861 < 2e-16 *** ## Groupb2Q -0.42429 0.02586 -16.410 < 2e-16 *** ## Groupb2W -0.73401 0.02616 -28.057 < 2e-16 *** ## --- ## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 ## ## (Dispersion parameter for binomial family taken to be 1) ## ## Null deviance: 67163 on 48491 degrees of freedom ## Residual deviance: 66279 on 48487 degrees of freedom ## AIC: 66289 ## ## Number of Fisher Scoring iterations: 4 ## OR 2.5 % 97.5 % ## (Intercept) 1.3055858 1.2590807 1.353875e+00 ## Transcription 353.0366507 17.5064483 1.059278e+04 ## Groupb1W 0.7952834 0.7559861 8.366032e-01 ## Groupb2Q 0.6542313 0.6218882 6.882252e-01 ## Groupb2W 0.4799784 0.4559689 5.052116e-01 6.2.2 Promoters ## ## Call: ## glm(formula = H3K27ac_P ~ Transcription + Group, family = "binomial", ## data = corrdat, na.action = na.exclude) ## ## Coefficients: ## Estimate Std. Error z value Pr(>|z|) ## (Intercept) -0.12084 0.01825 -6.620 3.58e-11 *** ## Transcription 0.63709 0.83078 0.767 0.44317 ## Groupb1W -0.08051 0.02579 -3.122 0.00179 ** ## Groupb2Q -0.32665 0.02604 -12.546 < 2e-16 *** ## Groupb2W -0.58884 0.02654 -22.187 < 2e-16 *** ## --- ## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 ## ## (Dispersion parameter for binomial family taken to be 1) ## ## Null deviance: 65645 on 48491 degrees of freedom ## Residual deviance: 65037 on 48487 degrees of freedom ## AIC: 65047 ## ## Number of Fisher Scoring iterations: 4 ## OR 2.5 % 97.5 % ## (Intercept) 0.8861782 0.8550249 0.9184428 ## Transcription 1.8909677 0.3623550 10.5315474 ## Groupb1W 0.9226433 0.8771682 0.9704675 ## Groupb2Q 0.7213358 0.6854358 0.7590876 ## Groupb2W 0.5549721 0.5268221 0.5845828 6.3 H3K4me3 6.3.1 Gene bodies ## ## Call: ## glm(formula = H3K4me3_GB ~ Transcription + Group, family = "binomial", ## data = corrdat, na.action = na.exclude) ## ## Coefficients: ## Estimate Std. Error z value Pr(>|z|) ## (Intercept) 0.34155 0.01865 18.310 < 2e-16 *** ## Transcription 6.89945 1.80374 3.825 0.000131 *** ## Groupb1W -0.06428 0.02606 -2.467 0.013635 * ## Groupb2Q -0.31404 0.02590 -12.124 < 2e-16 *** ## Groupb2W -0.27871 0.02591 -10.758 < 2e-16 *** ## --- ## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 ## ## (Dispersion parameter for binomial family taken to be 1) ## ## Null deviance: 66811 on 48491 degrees of freedom ## Residual deviance: 66571 on 48487 degrees of freedom ## AIC: 66581 ## ## Number of Fisher Scoring iterations: 4 ## OR 2.5 % 97.5 % ## (Intercept) 1.4071207 1.3566493 1.459566e+00 ## Transcription 991.7309448 35.1738630 3.969657e+04 ## Groupb1W 0.9377463 0.8910530 9.868794e-01 ## Groupb2Q 0.7304884 0.6943170 7.685177e-01 ## Groupb2W 0.7567566 0.7192762 7.961654e-01 6.3.2 Promoters ## ## Call: ## glm(formula = H3K4me3_P ~ Transcription + Group, family = "binomial", ## data = corrdat, na.action = na.exclude) ## ## Coefficients: ## Estimate Std. Error z value Pr(>|z|) ## (Intercept) -0.03695 0.01822 -2.028 0.04257 * ## Transcription 0.48051 0.83121 0.578 0.56321 ## Groupb1W 0.07629 0.02570 2.968 0.00299 ** ## Groupb2Q -0.11694 0.02573 -4.545 5.5e-06 *** ## Groupb2W -0.02362 0.02570 -0.919 0.35800 ## --- ## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 ## ## (Dispersion parameter for binomial family taken to be 1) ## ## Null deviance: 67191 on 48491 degrees of freedom ## Residual deviance: 67133 on 48487 degrees of freedom ## AIC: 67143 ## ## Number of Fisher Scoring iterations: 3 ## OR 2.5 % 97.5 % ## (Intercept) 0.9637213 0.9299038 0.9987600 ## Transcription 1.6168956 0.3181529 9.2732218 ## Groupb1W 1.0792802 1.0262608 1.1350481 ## Groupb2Q 0.8896392 0.8458815 0.9356488 ## Groupb2W 0.9766560 0.9286814 1.0271063 6.4 Comparison to random peaks Randomized peaks of the same quantity and average length in each sample group as the true peak set were generated with bedtools random for comparison. 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