ArticleScientific reports2019
A framework for identification of on- and off-target transcriptional responses to drug treatment.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Computational Drug Repositioning in Cardiorenal Disease: Opportunities, Challenges, and Approaches.Proteomics · 2025Article
- Expression of the aryl hydrocarbon receptor in Osterix-lineage cells regulates adult skeletal homeostasis in a compartment-specific manner.JBMR plus · 2025Article
- Embryotoxicity of statins and other prescribed drugs with reported off-target effects on cholesterol biosynthesis.Reproductive toxicology (Elmsford, N.Y.) · 2025Article
- Deciphering single-cell gene expression variability and its role in drug response.Human molecular genetics · 2024Article
- De novo drug design through gradient-based regularized search in information-theoretically controlled latent space.Journal of computer-aided molecular design · 2024Article
- Anti-Acinetobacter Baumannii single-chain variable fragments provide therapeutic efficacy in an immunocompromised mouse pneumonia model.BMC microbiology · 2024Article
- Contrastive learning in protein language space predicts interactions between drugs and protein targets.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Relationship between drug targets and drug-signature networks: a network-based genome-wide landscape.BMC medical genomics · 2023Article
- Ultraviolet light oxidation of fresh hemoglobin eliminates aggregate formation seen in commercially sourced hemoglobin.Blood cells, molecules & diseases · 2023Article
- Roles of Cofactors in Drug-Induced Liver Injury: Drug Metabolism and Beyond.Drug metabolism and disposition: the biological fate of chemicals · 2022Review
- Article
- FAK Inhibition Attenuates Corneal Fibroblast Differentiation In Vitro.Biomolecules · 2021Article
- DeepCellState: An autoencoder-based framework for predicting cell type specific transcriptional states induced by drug treatment.PLoS computational biology · 2021Article
- Emerging Therapeutic Potential of SIRT6 Modulators.Journal of medicinal chemistry · 2021Review
- Prevention of Post-Operative Adhesions: A Comprehensive Review of Present and Emerging Strategies.Biomolecules · 2021Review
- Establishing an Analogue Based In Silico Pipeline in the Pursuit of Novel Inhibitory Scaffolds against the SARS Coronavirus 2 Papain-Like Protease.Molecules (Basel, Switzerland) · 2021Article
- Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning.Cancers · 2020Review
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Owing to safety concerns or insufficient efficacy, few drug candidates are approved for marketing. Drugs already on the market may be withdrawn due to adverse effects (AEs) discovered after market introduction. Comprehensively investigating the on-/off-target effects of drugs can help expose AEs during the drug development process. We have developed an integrative framework for systematic identification of on-/off-target pathways and elucidation of the underlying regulatory mechanisms, by combining promoter expression profiling after drug treatment with gene perturbation of the primary drug target. Expression profiles from statin-treated cells and HMG-CoA reductase knockdowns were analyzed using the framework, allowing for identification of not only reported adverse effects but also novel candidates of off-target effects from statin treatment, including key regulatory elements of on- and off-targets. Our findings may provide new insights for finding new usages or potential side effects of drug treatment.
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