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Additional optimization code (MATLAB). (TXT 2Â kb)

This dataset contains the raw, unprocessed immunofluorescence, live-cell imaging and Western blot data for the manuscript entitled: Interactome rewiring following pharmacological targeting of BET bromodomains. All methods employed to generate this dataset can be found in the accompanying manuscript and supplemental material.

Additional file 10: Supplemental Table 2. Adjuvant treatments given to patients in the study cohort.

AUC results for low p/n data. Low p/n results for prediction accuracy using AUC as the performance metric for non-cross-validation results, 10-fold cross-validation and stratified 10-fold cross-validation. Ranks indicate the relative performance of different models with lower ranks representing higher performing models i.e., a rank of 1 is the best model. The default settings (n tree = 500, m try = 3, sampsize = 720) are found on row 1502 of the table. (CSV 116 kb)

Table S1A. All hydrogen deuterium exchange (HDX) peptide data for experiments examining the global exchange of PI4KIIIA, TTC7B, and FAM126A. The charge state (Z), residue start, residue end number, retention time (RT) and sequence are displayed for every peptide. In the Raw Data column, the two time points (0.3s and full) are labelled, and the relative level of HDX is coloured according to the amount of deuterium incorporated, on a blue to red continuum. The data listed for the 0.3s time point are the average of three independent experiments, with SD shown next to all HDX values. In the Normalized to Full Deuteration column, the 0.3s data has been normalised to the full deuteration measurements with the exception of those data (surrounded by black lines) where the full deuteration measurement was lower than 20% deuterium incorporation. The third column denotes the corresponding peptide centroid. Table S1B. All HDX peptide data for experiments examining the complex dynamics of PI4KIIIA, TTC7B, and FAM126A. The charge state (Z), residue start, residue end number, retention time (RT) and sequence are displayed for every peptide. The two columns represent each state examined (+/- PI4KIIIA) and contain the data for five time points. The data listed are the average of three independent experiments, with SD shown next to all HDX values. Table S1C. All HDX peptide data for experiments examining the dynamics of inhibitor specificity of PI4KIIIA, TTC7B, and FAM126A. The charge state (Z), residue start, residue end number, retention time (RT) and sequence are displayed for every peptide. The three columns represent each state examined (+/- inhibitor) and contain the data for four time points. The data listed are the average of three independent experiments, with SD shown next to all HDX values.

Additional file 2: Table S1. Details of the libraries generated from the Mütter Museum vaccination kits and vaccinia virus mapping statistics.

Additional file 4: Table S3. A. Results for 34 independent ARIC Discovery Meta-Analysis identified mtDNA-CN associated CpGs across all studied cohorts and Validation Meta-Analysis/All Cohort Meta-Analysis. Validation meta-analysis included CHS AA, CHS EA and FHS EA cohorts (P < 0.05 and same direction, bolded cells). All cohort meta-analysis (ARIC AA, ARIC EA, CHS AA, CHS EA and FHS EA) identified 6 validated CpGs (P < 5 × 10–8, shaded cells). B. Results for 23 independent ARIC AA identified CpGs across all studied cohorts. C. Results for 15 independent ARIC EA identified CpGs across all studied cohorts.

Additional file 2: Ontario Institute for Cancer Research (OICR) Tool Compound Library.