TGX – Toxicogenomics-based prediction and mechanism identification
In this case study a transcriptomics-based hazard prediction model for identification of specific molecular initiating events (MIE) will be applied based on (A) top-down and (B) bottom-up approaches.
The MIEs can include, but are not limited to: (1) Genotoxicity (p53 activation), (2) Oxidative stress (Nrf2 activation), (3) Endoplasmic Reticulum Stress (unfolded protein response), (4) Dioxin-like activity (AhR receptor activation), (5) HIF1 alpha activation and (6) Nuclear receptor activation (e.g. for endocrine disruption).
- Creation of prediction models based on differentially regulated genes (top-down approach);
- Using knowledge of stress response pathways to integrate data sets for their activation or inhibition (bottom-up approach).
Risk assessment framework
This case study is associated with all 3 tiers of the selected framework and in particular the following steps:
- Collection of support data;
- Identification of analogues / suitability assessment and existing data;
- Mode of Action hypothesis generation.
Use Cases Associated
This case study is associated with UC1 - Merge existing data by a common structure identifier and UC2 - Building and using a prediction model.
These two use cases are relevant for the top-down approaches:
- Reproducing the prediction models published by Herwig et al., 2016 using data from the EU-project carcinoGENOMICs;
- Advanced predictions using as much data as possible from the diXa data warehouse and other repositories giving free access to the data.
Databases and tools
- diXa (carcinoGENOMICs, Predict-IV), TG-GATEs, EU-ToxRisk (nascent), HeCaToS (nascent), ArrayExpress/GEO BioStudies.
- top-down: Data normalisation tools, prediction tools such as Caret;
- bottom-up: ToxPi.
Service integration will be needed for the omics databases; knowledge bases and data mining; processing and analysis.
Currently available services:
Service to run Nextflow pipelinesService type: Service, Workflow, Software
Interactive computing and workflows sharingService type: Helper tool, Visualisation tool, Processing tool, Analysis tool, Software, Workflow
Computation research made simple and reproducibleService type: Database / data source, Service, Workflow