TY - DATA T1 - Additional file 19: of Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription PY - 2015/10/08 AU - John Smestad AU - L. Maher UR - https://springernature.figshare.com/articles/dataset/Additional_file_19_of_Relationships_between_putative_G-quadruplex-forming_sequences_RecQ_helicases_and_transcription/4467257 DO - 10.6084/m9.figshare.c.3643949_D8.v1 L4 - https://ndownloader.figshare.com/files/7196720 KW - Additional KW - RecQ helicases KW - gene expression levels KW - FDR KW - bootstrapping simulations KW - gene expression KW - R 44 kb KW - G-quadruplex-forming sequences KW - gene sets KW - PQS position KW - regression model KW - PQS transcriptional effects KW - transcription R code KW - modeling prediction errors KW - epigenomic data N2 - R code for implementing epigenetic modeling of gene expression and analyzing PQS transcriptional effects. Program written in R that takes Additional files 12, 13, 14, 15, 16, 17, 18 as inputs and trains a Bayesian linear regression model upon epigenomic data to predict gene expression levels. Models are then applied to gene sets not used for training, and the subsequent sorting of modeling prediction errors by PQS position is used to calculate PQS transcriptional effects. Also conducts statistical bootstrapping simulations to estimate the FDR for this analysis. (R 44 kb) ER -