ArticlePLoS computational biology2019
Differential regulatory network-based quantification and prioritization of key genes underlying cancer drug resistance based on time-course RNA-seq data.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it, 26 citations in OpenAlex.
- Risk of Cardiac Adverse Events in Patients Treated With Immune Checkpoint Inhibitor Regimens: A Systematic Review and Meta-Analysis.Frontiers in oncology · 2021Pooled it
- Data-driven discovery of digital twins in biomedical research.Briefings in bioinformatics · 2026Review
- Cis-regulatory control of transcriptional timing and noise in response to estrogen.Cell genomics · 2024Article
- Article
- CSER: a gene regulatory network construction method based on causal strength and ensemble regression.Frontiers in genetics · 2024Article
- From time-series transcriptomics to gene regulatory networks: A review on inference methods.PLoS computational biology · 2023Review
- Patterns of Differentially Expressed circRNAs in Human Thymocytes.Non-coding RNA · 2022Article
- ORN: Inferring patient-specific dysregulation status of pathway modules in cancer with OR-gate Network.PLoS computational biology · 2021Article
- Review
- Omics and Computational Modeling Approaches for the Effective Treatment of Drug-Resistant Cancer Cells.Frontiers in genetics · 2021Review
- Exosome-Depleted Excretory-Secretory Products of the Fourth-Stage LarvalFrontiers in immunology · 2021Article
- Intracellular and Intercellular Gene Regulatory Network Inference From Time-Course Individual RNA-Seq.Frontiers in bioinformatics · 2021Article
- Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods.PloS one · 2021Article
- Data integration for inferring context-specific gene regulatory networks.Current opinion in systems biology · 2020Article
- DRIM: A Web-Based System for Investigating Drug Response at the Molecular Level by Condition-Specific Multi-Omics Data Integration.Frontiers in genetics · 2020Article
- Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Drug resistance is a major cause for the failure of cancer chemotherapy or targeted therapy. However, the molecular regulatory mechanisms controlling the dynamic evolvement of drug resistance remain poorly understood. Thus, it is important to develop methods for identifying key gene regulatory mechanisms of the resistance to specific drugs. In this study, we developed a data-driven computational framework, DryNetMC, using a differential regulatory network-based modeling and characterization strategy to quantify and prioritize key genes underlying cancer drug resistance. The DryNetMC does not only infer gene regulatory networks (GRNs) via an integrated approach, but also characterizes and quantifies dynamical network properties for measuring node importance. We used time-course RNA-seq data from glioma cells treated with dbcAMP (a cAMP activator) as a realistic case to reconstruct the GRNs for sensitive and resistant cells. Based on a novel node importance index that comprehensively quantifies network topology, network entropy and expression dynamics, the top ranked genes were verified to be predictive of the drug sensitivities of different glioma cell lines, in comparison with other existing methods. The proposed method provides a quantitative approach to gain insights into the dynamic adaptation and regulatory mechanisms of cancer drug resistance and sheds light on the design of novel biomarkers or targets for predicting or overcoming drug resistance.
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