ArticleToxicological sciences : an official journal of the Society of Toxicology2023
CTD tetramers: a new online tool that computationally links curated chemicals, genes, phenotypes, and diseases to inform molecular mechanisms for environmental health.
Article in Toxicological sciences : an official journal of the Society of Toxicology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43 citing papers in PubMed.
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- ToxiTaRGET: a multi-omics database for toxicant-responsive molecular targets.Nature communications · 2026Article
- Use of Computational Models to Investigate Human Targets of Small Ubiquitous Molecules.Chembiochem : a European journal of chemical biology · 2026Article
- A network-based map of the chemical exposome connects molecular interactions to public health.Nature communications · 2026Article
- DHGCMDA: a dual-view heterogeneous graph contrastive learning framework for miRNA-disease association type prediction.BMC bioinformatics · 2026Article
- Piperlongumine Inhibits Malignant Progression of Esophageal Squamous Cells Through the PI3K/AKT Signaling Pathway.Biochemical genetics · 2026Article
- From General-Purpose to Disease-Specific Features: Aligning LLM Embeddings on a Disease-Specific Biomedical Knowledge Graph for Drug Repurposing.bioRxiv : the preprint server for biology · 2026Article
- Integrated network pharmacology and bioinformatics analysis reveals MME as key target of Notoginsenoside R1 in diabetic nephropathy.BMC complementary medicine and therapies · 2026Article
- Integrative transcriptomic and genomic insights into diabetic kidney disease: evidence from multi-omics analysis and experimental validation.Renal failure · 2025Article
- Molecular mechanisms of olanzapine against agitation in schizophrenia and bipolar disorder based on network pharmacology and molecular docking.Scientific reports · 2025Article
- Therapeutic Role of Quercetin in Prostate Cancer: A Study of Network Pharmacology, Molecular Docking, and Dynamics Simulation.Cell biochemistry and biophysics · 2025Article
- BioWalk-MDA: a novel approach for large-scale predicting metabolite-drug associations based on multi layered biomedical knowledge graphs.Briefings in bioinformatics · 2025Article
- Quantifying compatibility mechanisms in traditional Chinese medicine with interpretable graph neural networks.Journal of pharmaceutical analysis · 2025Article
- Protective effect of micheliolide against inflammation and oxidative stress in asthma through the MAPK/NF-κB signalling pathway.The World Allergy Organization journal · 2025Article
- Bioinformatics Approach to Identifying Molecular Targets of Isoliquiritigenin Affecting Chronic Obstructive Pulmonary Disease: A Machine Learning Pharmacology Study.International journal of molecular sciences · 2025Article
- Regulatory trends of organophosphate and pyrethroid pesticides in cannabis and applications of the Comparative Toxicogenomics Database and Caenorhabditis elegans.Toxicological sciences : an official journal of the Society of Toxicology · 2025Article
- Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database.Database : the journal of biological databases and curation · 2025Article
- An integrative analysis reveals cancer risk associated with artificial sweeteners.Journal of translational medicine · 2025Article
- Article
- Unveiling esophageal cancer treatment mechanisms: network pharmacology and molecular docking of Physcion.Naunyn-Schmiedeberg's archives of pharmacology · 2025Article
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10 authors.
Funding
Abstract
The molecular mechanisms connecting environmental exposures to adverse endpoints are often unknown, reflecting knowledge gaps. At the Comparative Toxicogenomics Database (CTD), we developed a bioinformatics approach that integrates manually curated, literature-based interactions from CTD to generate a "CGPD-tetramer": a 4-unit block of information organized as a step-wise molecular mechanism linking an initiating Chemical, an interacting Gene, a Phenotype, and a Disease outcome. Here, we describe a novel, user-friendly tool called CTD Tetramers that generates these evidence-based CGPD-tetramers for any curated chemical, gene, phenotype, or disease of interest. Tetramers offer potential solutions for the unknown underlying mechanisms and intermediary phenotypes connecting a chemical exposure to a disease. Additionally, multiple tetramers can be assembled to construct detailed modes-of-action for chemical-induced disease pathways. As well, tetramers can help inform environmental influences on adverse outcome pathways (AOPs). We demonstrate the tool's utility with relevant use cases for a variety of environmental chemicals (eg, perfluoroalkyl substances, bisphenol A), phenotypes (eg, apoptosis, spermatogenesis, inflammatory response), and diseases (eg, asthma, obesity, male infertility). Finally, we map AOP adverse outcome terms to corresponding CTD terms, allowing users to query for tetramers that can help augment AOP pathways with additional stressors, genes, and phenotypes, as well as formulate potential AOP disease networks (eg, liver cirrhosis and prostate cancer). This novel tool, as part of the complete suite of tools offered at CTD, provides users with computational datasets and their supporting evidence to potentially fill exposure knowledge gaps and develop testable hypotheses about environmental health.
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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.