Development of a Genetic Priority Score to Predict Drug Side Effects Using Human Genetic Evidence

This Zenodo repository contains the data associated with the publication:

Duffy, Á et al. Development of a Genetic Priority Score to Predict Drug Side Effects Using Human Genetic Evidence. Submitted

You can explore these scores further at https://rstudio-connect.hpc.mssm.edu/sideeffect-geneticpriorityscore/.

Repository contents

This archive contains all data necessary to reproduce the analyses described in the manuscript. The corresponding analysis scripts can be cloned from https://github.com/rondolab/SE-GPS.

Files within Data.zip include:

• Processed drug–genetic datasets at the drug-gene-parentterm level:
• Opentargets_dataset_se.mi_withgeneticsfiltered_5_All_parentterm_drugse_final.txt.gz
• Onsides_dataset_se.mi_withgeneticsfiltered_5_All_parentterm_drugse_final.txt.gz
• Severe drug side effect subset:
• Withdrawndrugs_dataset_Opentargets_outcome_senomi_phase4.txt
• Opentargets_dataset_drugwarnings_filtered_5_All_drugse_final.txt
• Withdrawndrugs_dataset_Onsides_outcome_senomi_phase4.txt
• Onsides_dataset_drugwarnings_filtered_5_All_drugse_final.txt
• Severity scoring files:
• Adr_severity_scores_phecodeX.txt
• PhecodeX information:
• phecodeX_info.csv
• All gene dataset for 19,422 protein-coding genes and 502 phecodes
• Allgenes_dataset_parentterm_predictors_collapsed_sideeffect_project.txt.gz
• Allgenes_dataset_phenotype_predictors_stringentfilters_sideeffect_project.txt.gz
• LOF and GOF evidence for each feature:
• Predictors_with_direction_effect_sideeffect_project_gof_predvalue.txt
• Predictors_with_direction_effect_sideeffect_project_lof_predvalue.txt
• Processed drug–genetic datasets with directional evidence
• Opentargetsgeneticdataset_filtered_5_All_DOE_matchmechanism.txt.gz
• Onsidesgeneticdataset_filtered_5_All_DOE_matchmechanism.txt.gz

Note, we use the word parentterm to refer to the phecodeX integer.