References

DoseRider is a bioinformatics web tool that utilizes various datasets, gene sets, and R libraries for its analyses. Below are the relevant citations for the resources used in DoseRider:

Datasets

  • PRJNA869442:
    Matteo G, Leingartner K, Rowan-Carroll A, et al. In vitro transcriptomic analyses reveal pathway perturbations, estrogenic activities, and potencies of data-poor BPA alternative chemicals. Toxicol Sci. 2023 Feb 17;191(2):266-275. doi: 10.1093/toxsci/kfac127. PMID: 36534918; PMCID: PMC9936204.
  • PRJNA391282:
    Zhou YH, Cichocki JA, Soldatow VY, et al. Comparative Dose-Response Analysis of Liver and Kidney Transcriptomic Effects of Trichloroethylene and Tetrachloroethylene in B6C3F1 Mouse. Toxicol Sci. 2017 Nov 1;160(1):95-110. doi: 10.1093/toxsci/kfx165. PMID: 28973375; PMCID: PMC5837274.
  • Zhao2022 (BPA Dose-Response Metabolomics):
    Zhao H, Liu M, Lv Y, Fang M. Dose-response metabolomics and pathway sensitivity to map molecular cartography of bisphenol A exposure. Environ Int. 2022 Jan;158:106893. doi: 10.1016/j.envint.2021.106893. Epub 2021 Sep 27. PMID: 34592654.
  • E-TABM-585:
    Ji RR, de Silva H, Jin Y, et al. Transcriptional Profiling of the Dose Response: A More Powerful Approach for Characterizing Drug Activities. PLoS Comput Biol. 2009 Sep;5(9):e1000512. doi: 10.1371/journal.pcbi.1000512. PMID: 19763178; PMCID: PMC2731201.

Gene Sets

  • ConsensusPathDB:
    Kamburov A, Herwig R. ConsensusPathDB 2022: molecular interactions update as a resource for network biology. Nucleic Acids Res. 2022 Jan 7;50(D1):D587-D595. doi: 10.1093/nar/gkab1128. PMID: 34850110; PMCID: PMC8728246.
  • MSigDB:
    Castanza AS, Recla JM, Eby D, et al. Extending support for mouse data in the Molecular Signatures Database (MSigDB). Nat Methods. 2023;20:1619–1620. doi: 10.1038/s41592-023-02014-7.
    Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-15550. doi: 10.1073/pnas.0506580102. PMID: 16199517; PMCID: PMC1239896.
  • MIO (Immune-Related Gene Signatures):
    Monfort-Lanzas P, Gronauer R, Madersbacher L, et al. MIO: microRNA target analysis system for immuno-oncology. Bioinformatics. 2022 Jul;38(14):3665-3667. doi: 10.1093/bioinformatics/btac366. MIO Website

R Libraries

  • lme4 (for Statistical Analysis):
    Bates D, Mächler M, Bolker B, Walker S. Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software. 2015;67(1):1-48. doi: 10.18637/jss.v067.i01.
  • ComplexHeatmap (for Visualization):
    Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32(18):2847-2849. doi: 10.1093/bioinformatics/btw313.

Webserver Development

  • The DoseRider webserver was developed using the Django framework.

We would like to acknowledge and thank the developers of these tools and datasets for providing invaluable resources that significantly contributed to the development of DoseRider.