ToxDAR: A Workflow Software for Analyzing Toxicologically Relevant Proteomic and Transcriptomic Data, from Data Preparation to Toxicological Mechanism Elucidation
Abstract
:1. Introduction
2. Result
2.1. Software Framework
2.2. Software Function
2.3. Research Case: Toxicological Mechanism Analysis of Public Transcriptome Data in L02 Cell Line Post-Triphenyl Phosphate (TPP) Exposure
3. Discussion
4. Materials and Methods
4.1. Primary Functions
4.2. Data Sources
4.3. Toxicological Classification System
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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External Software Package | Version | Functionality |
---|---|---|
NormExpression | V0.1.0 | getNormMatrix; gatherCVs |
ggord | V1.1.7 | ggord.pca |
limma | V3.54.2 | model.matrix; lmFit; eBayes |
clusterProfiler | V4.6.2 | enricher |
org.Hs.eg.db | V3.16.0 | org.Hs.eg.db |
gprofiler2 | V0.2.1 | gconvert |
fgsea | V1.24.0 | fgsea; plotEnrichment |
igraph | V1.3.5 | graph_from_edgelist; clusters;layout |
msigdbr | V7.5.1 | msigdbr |
ComplexHeatmap | V2.14.0 | rowAnnotation; Heatmap |
dplyr | V1.0.10 | mutate;select; group_by |
ggplot2 | V3.4.0 | ggplot; ggtitle; theme; geom_point; geom_hline |
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Human Phenotype Ontology | v2021-10-10 | https://hpo.jax.org/app/, accessed on 10 October 2022. |
PhosphoSitePlus | v6.6 | https://www.phosphosite.org/ |
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Jiang, P.; Zhang, Z.; Yu, Q.; Wang, Z.; Diao, L.; Li, D. ToxDAR: A Workflow Software for Analyzing Toxicologically Relevant Proteomic and Transcriptomic Data, from Data Preparation to Toxicological Mechanism Elucidation. Int. J. Mol. Sci. 2024, 25, 9544. https://doi.org/10.3390/ijms25179544
Jiang P, Zhang Z, Yu Q, Wang Z, Diao L, Li D. ToxDAR: A Workflow Software for Analyzing Toxicologically Relevant Proteomic and Transcriptomic Data, from Data Preparation to Toxicological Mechanism Elucidation. International Journal of Molecular Sciences. 2024; 25(17):9544. https://doi.org/10.3390/ijms25179544
Chicago/Turabian StyleJiang, Peng, Zuzhen Zhang, Qing Yu, Ze Wang, Lihong Diao, and Dong Li. 2024. "ToxDAR: A Workflow Software for Analyzing Toxicologically Relevant Proteomic and Transcriptomic Data, from Data Preparation to Toxicological Mechanism Elucidation" International Journal of Molecular Sciences 25, no. 17: 9544. https://doi.org/10.3390/ijms25179544