Open Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system

Names
More detailed information about this field from each metasource.

Open Toxicogenomics Project-Genomics Assisted Toxicity Evaluation system
metasource: Fairsharing.org
version: None

Open TG-GATEs
metasource: Fairsharing.org
version: None

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Open TG-GATEs API
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:09.508344

open_tg-gates
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:09.508344

Other names: Open TG-GATEs, Open TG-GATEs API, open_tg-gates

This source may no longer be available. No known URL could be resolved successfully.

Open TG-GATEs is a public toxicogenomics database developed so that a wider community of researchers could utilize the fruits of TGP and TGP2 research. This database provides public access to data on 170 of the compounds catalogued in TG-GATEs. Data searching can be refined using either the name of a compound or the pathological findings by organ as the starting point. Gene expression data linked to phenotype data in pathology findings can also be downloaded as a CEL(*)file.

Webpage:

http://toxico.nibiohn.go.jp/english/

Licence:

Name: Open TG-GATEs Database License
URL: http://toxico.nibiohn.go.jp/english/agreement.html

Publications:

Publications
More detailed information about this field from each metasource.

Open TG-GATEs: a large-scale toxicogenomics database
PMID: 25313160
metasource: Fairsharing.org
version: None

http://dx.doi.org/10.1093/nar/gku955
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:09.508344

Open TG-GATEs: a large-scale toxicogenomics database PubMed citations: 133.

133 articles citing: Open TG-GATEs: a large-scale toxicogenomics database

Semi-automated approach for generation of biological networks on drug-induced cholestasis, steatosis, hepatitis, and cirrhosis. PMID:35865277
A genome-wide screen for resilient responses in growing pigs. PMID:35787790
In silico approaches in organ toxicity hazard assessment: Current status and future needs for predicting heart, kidney and lung toxicities. PMID:35721273
Network approaches for modeling the effect of drugs and diseases. PMID:35704883
Current Therapeutic Landscape and Safety Roadmap for Targeting the Aryl Hydrocarbon Receptor in Inflammatory Gastrointestinal Indications. PMID:35626744
The development and application of in silico models for drug induced liver injury. PMID:35542036
Integration of Adverse Outcome Pathways, Causal Networks and 'Omics to Support Chemical Hazard Assessment. PMID:35399296
Nextcast: A software suite to analyse and model toxicogenomics data. PMID:35386103
Computational analyses of mechanism of action (MoA): data, methods and integration. PMID:35360890
PharmOmics: A species- and tissue-specific drug signature database and gene-network-based drug repositioning tool. PMID:35345455
Integrative omics - An arsenal for drug discovery. PMID:35343200
In silico approaches in organ toxicity hazard assessment: current status and future needs in predicting liver toxicity. PMID:35340402
From Causal Networks to Adverse Outcome Pathways: A Developmental Neurotoxicity Case Study. PMID:35295214
Emerging Bioinformatics Methods and Resources in Drug Toxicology. PMID:35188631
A computational system for Bayesian benchmark dose estimation of genomic data in BBMD. PMID:35151117
EDTox: an R Shiny application to predict the endocrine disruption potential of compounds. PMID:35134136
Knowledge-Driven Approaches to Create the MTox700+ Metabolite Panel for Predicting Toxicity. PMID:35094093
Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses. PMID:35073843
Preclinical models of idiosyncratic drug-induced liver injury (iDILI): Moving towards prediction. PMID:35024301
Integrated Genomic and Bioinformatics Approaches to Identify Molecular Links between Endocrine Disruptors and Adverse Outcomes. PMID:35010832
Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation. PMID:34962256
Artificial intelligence in clinical research of cancers. PMID:34929741
Mapping the cellular response to electron transport chain inhibitors reveals selective signaling networks triggered by mitochondrial perturbation. PMID:34642769
The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment. PMID:34626214
Orchestrating and sharing large multimodal data for transparent and reproducible research. PMID:34608132
Cell type-specific potential pathogenic genes and functional pathways in Alzheimer's Disease. PMID:34600516
Reproducibility and robustness of high-throughput S1500+ transcriptomics on primary rat hepatocytes for chemical-induced hepatotoxicity assessment. PMID:34467220
Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology. PMID:34333066
Multi-resolution characterization of molecular taxonomies in bulk and single-cell transcriptomics data. PMID:34226941
Predictive modeling of biological responses in the rat liver using in vitro Tox21 bioactivity: Benefits from high-throughput toxicokinetics. PMID:34013136
SARS-CoV-2 Switches 'on' MAPK and NFκB Signaling via the Reduction of Nuclear DUSP1 and DUSP5 Expression. PMID:33995033
Colchicine acts selectively in the liver to induce hepatokines that inhibit myeloid cell activation. PMID:33846641
The eTRANSAFE Project on Translational Safety Assessment through Integrative Knowledge Management: Achievements and Perspectives. PMID:33800393
TOXPANEL: A Gene-Set Analysis Tool to Assess Liver and Kidney Injuries. PMID:33633572
Evaluation of the Use of Single- and Multi-Magnification Convolutional Neural Networks for the Determination and Quantitation of Lesions in Nonclinical Pathology Studies. PMID:33618634
Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 2: a discussion of chemical and biological data. PMID:33508423
Mexican Ganoderma Lucidum Extracts Decrease Lipogenesis Modulating Transcriptional Metabolic Networks and Gut Microbiota in C57BL/6 Mice Fed with a High-Cholesterol Diet. PMID:33374283
Deep Learning on High-Throughput Transcriptomics to Predict Drug-Induced Liver Injury. PMID:33330410
Identification of early liver toxicity gene biomarkers using comparative supervised machine learning. PMID:33154507
Drivers of and Obstacles to the Adoption of Toxicogenomics for Chemical Risk Assessment: Insights from Social Science Perspectives. PMID:33112659
Thresholds Derived From Common Measures in Rat Studies Are Predictive of Liver Tumorigenic Chemicals. PMID:33084515
Embedding covariate adjustments in tree-based automated machine learning for biomedical big data analyses. PMID:32998684
Polygenic architecture informs potential vulnerability to drug-induced liver injury. PMID:32895570
The regulatory role of PGC1α-related coactivator in response to drug-induced liver injury. PMID:32821877
Effect of common medications on the expression of SARS-CoV-2 entry receptors in liver tissue. PMID:32808185
Effect of Common Medications on the Expression of SARS-CoV-2 Entry Receptors in Kidney Tissue. PMID:32799423
Use of deep learning methods to translate drug-induced gene expression changes from rat to human primary hepatocytes. PMID:32780735
Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing. PMID:32656864
Valproic acid promotes mitochondrial dysfunction in primary human hepatocytes in vitro; impact of C/EBPα-controlled gene expression. PMID:32623605
A Set of Six Gene Expression Biomarkers Identify Rat Liver Tumorigens in Short-term Assays. PMID:32603430
Application of a Rat Liver Drug Bioactivation Transcriptional Response Assay Early in Drug Development That Informs Chemically Reactive Metabolite Formation and Potential for Drug-induced Liver Injury. PMID:32559301
WERFE: A Gene Selection Algorithm Based on Recursive Feature Elimination and Ensemble Strategy. PMID:32548100
Concordance between Thioacetamide-Induced Liver Injury in Rat and Human In Vitro Gene Expression Data. PMID:32512829
Scoring functions for drug-effect similarity. PMID:32484516
TinderMIX: Time-dose integrated modelling of toxicogenomics data. PMID:32449777
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets. PMID:32421831
Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data. PMID:32397130
Applying knowledge-driven mechanistic inference to toxicogenomics. PMID:32387679
A Rat Liver Transcriptomic Point of Departure Predicts a Prospective Liver or Non-liver Apical Point of Departure. PMID:32384157
The EDCMET Project: Metabolic Effects of Endocrine Disruptors. PMID:32344727
Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects. PMID:32326418
Using FFPE RNA-Seq with 12 marker genes to evaluate genotoxic and non-genotoxic rat hepatocarcinogens. PMID:32256870
NanoSolveIT Project: Driving nanoinformatics research to develop innovative and integrated tools for in silico nanosafety assessment. PMID:32226594
Narrowing the Gap Between In Vitro and In Vivo Genetic Profiles by Deconvoluting Toxicogenomic Data In Silico. PMID:31992983
Assessing Chemical-Induced Liver Injury In Vivo From In Vitro Gene Expression Data in the Rat: The Case of Thioacetamide Toxicity. PMID:31850077
An omics perspective on drug target discovery platforms. PMID:31774113
Genome-Scale Model-Based Identification of Metabolite Indicators for Early Detection of Kidney Toxicity. PMID:31722432
T1000: a reduced gene set prioritized for toxicogenomic studies. PMID:31681519
Mining Public Toxicogenomic Data Reveals Insights and Challenges in Delineating Liver Steatosis Adverse Outcome Pathways. PMID:31681434
CLINE: a web-tool for the comparison of biological dendrogram structures. PMID:31660851
Comparison of Gene Expression Responses in the Small Intestine of Mice Following Exposure to 3 Carcinogens Using the S1500+ Gene Set Informs a Potential Common Adverse Outcome Pathway. PMID:31558096
DynOVis: a web tool to study dynamic perturbations for capturing dose-over-time effects in biological networks. PMID:31409281
Assessment of Drugs Toxicity and Associated Biomarker Genes Using Hierarchical Clustering. PMID:31398888
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. PMID:31244651
Automated Machine Learning Diagnostic Support System as a Computational Biomarker for Detecting Drug-Induced Liver Injury Patterns in Whole Slide Liver Pathology Images. PMID:31149832
A Novel Open Access Web Portal for Integrating Mechanistic and Toxicogenomic Study Results. PMID:31020328
Mechanistic identification of biofluid metabolite changes as markers of acetaminophen-induced liver toxicity in rats. PMID:30974156
Frequent Modulation of the Sterol Regulatory Element Binding Protein (SREBP) by Chemical Exposure in the Livers of Rats. PMID:30931410
Assessment of a Highly Multiplexed RNA Sequencing Platform and Comparison to Existing High-Throughput Gene Expression Profiling Techniques. PMID:30891063
Deep Neural Network Models for Predicting Chemically Induced Liver Toxicity Endpoints From Transcriptomic Responses. PMID:30804783
Unsupervised identification of disease states from high-dimensional physiological and histopathological profiles. PMID:30782979
Literature optimized integration of gene expression for organ-specific evaluation of toxicogenomics datasets. PMID:30640953
NBDC RDF portal: a comprehensive repository for semantic data in life sciences. PMID:30576482
Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury. PMID:30515189
Identification of the Toxicity Pathways Associated With Thioacetamide-Induced Injuries in Rat Liver and Kidney. PMID:30459623
Robust Co-clustering to Discover Toxicogenomic Biomarkers and Their Regulatory Doses of Chemical Compounds Using Logistic Probabilistic Hidden Variable Model. PMID:30450112
Characterisation of the NRF2 transcriptional network and its response to chemical insult in primary human hepatocytes: implications for prediction of drug-induced liver injury. PMID:30426165
A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples. PMID:30420870
Investigation of Nrf2, AhR and ATF4 Activation in Toxicogenomic Databases. PMID:30333853
A Qualitative Modeling Approach for Whole Genome Prediction Using High-Throughput Toxicogenomics Data and Pathway-Based Validation. PMID:30333746
Analysis of Time-Series Gene Expression Data to Explore Mechanisms of Chemical-Induced Hepatic Steatosis Toxicity. PMID:30279702
Role of xenobiotics in the induction and progression of fatty liver disease. PMID:30090613
PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies. PMID:30053271
ChemDIS 2: an update of chemical-disease inference system. PMID:30053236
Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. PMID:29917034
Decision Variants for the Automatic Determination of Optimal Feature Subset in RF-RFE. PMID:29914084
In silico cancer research towards 3R. PMID:29649981
Transcriptional Responses Reveal Similarities Between Preclinical Rat Liver Testing Systems. PMID:29616076
A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics. PMID:29462216
Ab initio chemical safety assessment: A workflow based on exposure considerations and non-animal methods. PMID:29214231
A Pipeline for High-Throughput Concentration Response Modeling of Gene Expression for Toxicogenomics. PMID:29163636
Overcoming Obstacles to Drug Repositioning in Japan. PMID:29075191
A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury. PMID:28671182
Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates. PMID:28469246
A computational toxicogenomics approach identifies a list of highly hepatotoxic compounds from a large microarray database. PMID:28448553
Toxicogenomic module associations with pathogenesis: a network-based approach to understanding drug toxicity. PMID:28440344
Inferring Genes and Biological Functions That Are Sensitive to the Severity of Toxicity Symptoms. PMID:28368331
Applying evolutionary genetics to developmental toxicology and risk assessment. PMID:28267574
Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions. PMID:28176778
A Comparative Analysis of Drug-Induced Hepatotoxicity in Clinically Relevant Situations. PMID:28151932
Multiscale modeling reveals inhibitory and stimulatory effects of caffeine on acetaminophen-induced toxicity in humans. PMID:28130915
Elucidating the modes of action for bioactive compounds in a cell-specific manner by large-scale chemically-induced transcriptomics. PMID:28071740
DTNI: a novel toxicogenomics data analysis tool for identifying the molecular mechanisms underlying the adverse effects of toxic compounds. PMID:28032149
Genomic Characterization of Metformin Hepatic Response. PMID:27902686
CEBS: a comprehensive annotated database of toxicological data. PMID:27899660
Prediction of Non-Genotoxic Carcinogenicity Based on Genetic Profiles of Short Term Exposure Assays. PMID:27818731
Gene expression data from acetaminophen-induced toxicity in human hepatic in vitro systems and clinical liver samples. PMID:27761495
Evaluation of an Hprt-Luciferase Reporter Gene on a Mammalian Artificial Chromosome in Response to Cytotoxicity. PMID:27493490
Collaborative studies in toxicogenomics in rodent liver in JEMS·MMS; a useful application of principal component analysis on toxicogenomics. PMID:27482301
Research Resource: A Reference Transcriptome for Constitutive Androstane Receptor and Pregnane X Receptor Xenobiotic Signaling. PMID:27409825
Model-based contextualization of in vitro toxicity data quantitatively predicts in vivo drug response in patients. PMID:27161439
ToxDB: pathway-level interpretation of drug-treatment data. PMID:27074805
Plasma lipid profiling of different types of hepatic fibrosis induced by carbon tetrachloride and lomustine in rats. PMID:27068811
Mechanistically linked serum miRNAs distinguish between drug induced and fatty liver disease of different grades. PMID:27045805
Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes. PMID:27028627
Accelerating Adverse Outcome Pathway Development Using Publicly Available Data Sources. PMID:26809562
Systems toxicology of chemically induced liver and kidney injuries: histopathology-associated gene co-expression modules. PMID:26725466
Predicting target proteins for drug candidate compounds based on drug-induced gene expression data in a chemical structure-independent manner. PMID:26684652
OpenTein: a database of digital whole-slide images of stem cell-derived teratomas. PMID:26496950
Meta-Analysis of Large-Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of Drug-Induced Toxicity. PMID:26335687
Identification of in vitro and in vivo disconnects using transcriptomic data. PMID:26282683
Asymmetric author-topic model for knowledge discovering of big data in toxicogenomics. PMID:25941488
Pathway reporter genes define molecular phenotypes of human cells. PMID:25903797
http://dx.doi.org/10.1093/nar/gku955

Tags:

Tags
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gene expression data
metasource: Fairsharing.org
version: None

histology
metasource: Fairsharing.org
version: None

liver
metasource: Fairsharing.org
version: None

other molecular biology databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

drugs and drug design
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:09.508344

gene expression histology liver molecular biology drug genomics

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Comparative Toxicogenomics Database

Chemical Effects in Biological Systems

Toxic Process Ontology

Pharmacogenomics Knowledge Base

Manually Curated Database of Rice Proteins

Expression Atlas

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Rat Genome Database

StreptomeDB

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Open Science Framework

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Hepamine