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Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment.

Angela Serra1,2, Michele Fratello1,2, Luca Cattelani1,2

  • 1Faculty of Medicine and Health Technology, Tampere University, FI-33014 Tampere, Finland.

Nanomaterials (Basel, Switzerland)
|April 12, 2020
PubMed
Summary
This summary is machine-generated.

This review explores data modeling in toxicogenomics (TGx), focusing on transcriptomics. Advanced artificial intelligence (AI) and modeling techniques enhance chemical safety assessments using TGx data.

Keywords:
QSARbenchmark dose analysisdata integrationdata modellingdeep learningmachine learningnetwork analysisread-acrosstoxicogenomicstranscriptomics

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Area of Science:

  • Toxicogenomics
  • Transcriptomics
  • Computational Toxicology

Background:

  • Transcriptomics data offers valuable insights for toxicogenomics (TGx).
  • Increasing omics datasets and analytical methods facilitate TGx research.
  • AI methods are increasingly applied to analyze large TGx datasets.

Purpose of the Study:

  • To review the state-of-the-art in data modeling for transcriptomics in TGx.
  • To highlight the application of AI and advanced modeling techniques in TGx.
  • To discuss the role of TGx data modeling in chemical safety assessment.

Main Methods:

  • Review of benchmark dose (BMD) analysis in TGx.
  • Examination of read-across and adverse outcome pathway (AOP) modeling.
  • Discussion of network-based approaches for mechanism of action (MOA) and biomarker discovery.
  • Overview of artificial intelligence (AI) methodologies, including deep learning (DL) and data integration.

Main Results:

  • Data modeling, particularly with AI, is crucial for predictive toxicology using TGx data.
  • BMD analysis, read-across, AOPs, and network-based approaches are key TGx modeling tools.
  • AI and DL methods enable the development of robust predictive classification and regression models for TGx.

Conclusions:

  • Modeling of TGx transcriptomics data is essential for accurate chemical safety assessment.
  • Advanced computational approaches significantly enhance the utility of TGx data.
  • This review provides a comprehensive overview of current modeling strategies in TGx.