ArticleCPT: pharmacometrics & systems pharmacology2014
Systematic analysis of new drug indications by drug-gene-disease coherent subnetworks.
Article in CPT: pharmacometrics & systems pharmacology, 2014. 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.
- Detection of an anti-angina therapeutic module in the effective population treated by a multi-target drug Danhong injection: a randomized trial.Signal transduction and targeted therapy · 2021Trial
- Novel artificial intelligence-based identification of drug-gene-disease interaction using protein-protein interaction.BMC bioinformatics · 2024Article
- Targets preliminary screening for the fresh natural drug molecule based on Cosine-correlation and similarity-comparison of local network.Journal of translational medicine · 2022Article
- PPDTS: Predicting potential drug-target interactions based on network similarity.IET systems biology · 2022Article
- Circular RNAs and complex diseases: from experimental results to computational models.Briefings in bioinformatics · 2021Review
- Learning from low-rank multimodal representations for predicting disease-drug associations.BMC medical informatics and decision making · 2021Article
- The Complex Structure of the Pharmacological Drug-Disease Network.Entropy (Basel, Switzerland) · 2021Article
- A systems pharmacology approach based on oncogenic signalling pathways to determine the mechanisms of action of natural products in breast cancer from transcriptome data.BMC complementary medicine and therapies · 2021Article
- Genome-wide discovery of hidden genes mediating known drug-disease association using KDDANet.NPJ genomic medicine · 2021Article
- Transcriptome-based drug repositioning for coronavirus disease 2019 (COVID-19).Pathogens and disease · 2020Article
- Prediction of Potential Drug-Disease Associations through Deep Integration of Diversity and Projections of Various Drug Features.International journal of molecular sciences · 2019Article
- Systematical Identification of Breast Cancer-Related Circular RNA Modules for Deciphering circRNA Functions Based on the Non-Negative Matrix Factorization Algorithm.International journal of molecular sciences · 2019Article
- Predicting drug-disease associations by using similarity constrained matrix factorization.BMC bioinformatics · 2018Article
- Exploring traditional chinese medicine by a novel therapeutic concept of network target.Chinese journal of integrative medicine · 2016Article
- Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data.National science review · 2016Article
- Immunomediated Pan-cancer Regulation Networks are Dominant Fingerprints After Treatment of Cell Lines with Demethylation.Cancer informatics · 2016Article
- Multiscale Modeling of Drug-induced Effects of ReDuNing Injection on Human Disease: From Drug Molecules to Clinical Symptoms of Disease.Scientific reports · 2015Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Drug targets and disease genes may work as driver factors at the transcriptional level, which propagate signals through gene regulatory network and cause the downstream genes' differential expression. How to analyze transcriptional response data to identify meaningful gene modules shared by both drugs and diseases is still a critical issue for drug-disease associations and molecular mechanism. In this article, we propose the drug-gene-disease coherent subnetwork concept to group the biological function related drugs, diseases, and genes. It was defined as the subnetwork with drug, gene, and disease as nodes and their interactions coherently crossing three data layers as edges. Integrating differential expression profiles of 418 drugs and 84 diseases, we develop a computational framework and identify 13 coherent subnetworks such as inflammatory bowel disease and melanoma relevant subnetwork. The results demonstrate that our coherent subnetwork approach is able to identify novel drug indications and highlight their molecular basis.
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Registered trials
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