ArticleScientific reports2015
Drug target prioritization by perturbed gene expression and network information.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- A network medicine framework for multi-modal data integration in therapeutic target discovery.Communications chemistry · 2026Article
- Unlocking the potential of computational phenotypic drug discovery: methods, challenges, and future directions.NPJ systems biology and applications · 2026Review
- Harnessing AI to fuse phenotypic signatures for drug target identification: progress in computational modeling.Briefings in bioinformatics · 2026Review
- IID 2025: Physical protein interaction data with detection types, co-purified protein sets, molecular docking, and immune cell networks.Nucleic acids research · 2026Article
- In-silico discovery of druggable molecular signatures that drive dengue fever to severe dengue fever highlighting common pathogenesis through single-cell RNA-Seq analysis.Scientific reports · 2025Article
- Discovering anticancer drug target combinations via network-informed signaling-based approach.Communications medicine · 2025Article
- TnP as a Multifaceted Therapeutic Peptide with System-Wide Regulatory Capacity.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Target repositioning using multi-layer networks and machine learning: The case of prostate cancer.Computational and structural biotechnology journal · 2024Article
- Anticancer Target Combinations: Network-Informed Signaling-Based Approach to Discovery.bioRxiv : the preprint server for biology · 2024Article
- Herb-CMap: a multimodal fusion framework for deciphering the mechanisms of action in traditional Chinese medicine using Suhuang antitussive capsule as a case study.Briefings in bioinformatics · 2024Article
- scRank infers drug-responsive cell types from untreated scRNA-seq data using a target-perturbed gene regulatory network.Cell reports. Medicine · 2024Article
- Small molecule-mediated targeting of microRNAs for drug discovery: Experiments, computational techniques, and disease implications.European journal of medicinal chemistry · 2023Review
- DAIKON: A Data Acquisition, Integration, and Knowledge Capture Web Application for Target-Based Drug Discovery.ACS pharmacology & translational science · 2023Article
- A proteome-wide atlas of drug mechanism of action.Nature biotechnology · 2023Article
- On the correspondence between the transcriptomic response of a compound and its effects on its targets.BMC bioinformatics · 2023Article
- Investigating the potential anti-depressive mechanisms of statins: a transcriptomic and Mendelian randomization analysis.Translational psychiatry · 2023Article
- Relationship between drug targets and drug-signature networks: a network-based genome-wide landscape.BMC medical genomics · 2023Article
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- The module triad: a novel network biology approach to utilize patients' multi-omics data for target discovery in ulcerative colitis.Scientific reports · 2022Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Drugs bind to their target proteins, which interact with downstream effectors and ultimately perturb the transcriptome of a cancer cell. These perturbations reveal information about their source, i.e., drugs' targets. Here, we investigate whether these perturbations and protein interaction networks can uncover drug targets and key pathways. We performed the first systematic analysis of over 500 drugs from the Connectivity Map. First, we show that the gene expression of drug targets is usually not significantly affected by the drug perturbation. Hence, expression changes after drug treatment on their own are not sufficient to identify drug targets. However, ranking of candidate drug targets by network topological measures prioritizes the targets. We introduce a novel measure, local radiality, which combines perturbed genes and functional interaction network information. The new measure outperforms other methods in target prioritization and proposes cancer-specific pathways from drugs to affected genes for the first time. Local radiality identifies more diverse targets with fewer neighbors and possibly less side effects.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.