ToxDAR

ToxDAR preprocesses and analyzes toxicological multi-omics data through an integrated workflow that connects omics results to toxicological knowledge via a knowledge graph.

Key Features:

• Data Preparation and Quality Control: Supports preprocessing steps for toxicological multi-omics data.
• Differential Expression Analysis: Integrates DESeq2 and NormExpression for analyzing proteomic and transcriptomic data.
• Functional Analysis: Utilizes R functions including prcomp and phyper for statistical and functional analysis.
• Network Analysis: Integrates the igraph package for network-based analysis of toxicological data.
• Knowledge Graph Annotation: Contains five major categories of mechanism-related biological entities and fifteen types of interactions among them for comprehensive pathway annotation and toxicological mechanism elucidation.

Scientific Applications:

• Toxicological Mechanism Elucidation: Identifies biological pathways associated with toxicity and establishes connections between omics data and existing toxicological knowledge.
• Chemical Safety Assessment: Evaluates potential adverse reactions to chemicals and pharmaceutical agents.
• Drug Development Support: Aids in understanding toxic mechanisms to engineer safer compounds and discover new therapeutic targets.
• Transcriptomic Toxicology Analysis: Applied to analyze transcriptomic datasets such as triphenyl phosphate (TPP) toxicology, revealing impacts on thyroid function via thyroid hormone receptor beta (THRB) activation and pathways related to programmed cell death and inflammation.

Methodology:

ToxDAR integrates R packages including NormExpression, DESeq2, and igraph, and utilizes R functions such as prcomp and phyper.