ArticleBioinformatics (Oxford, England)2025
DOSE-L1000-Viz: an interactive Shiny application for dose-response transcriptomic analysis, target-centric exploration, and signature search.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
summaryUnderstanding how small molecules perturb gene expression is critical for guiding drug discovery. We present DOSE-L1000-Viz, a Shiny application that facilitates comprehensive exploration of compound-induced transcriptomic responses across doses, time points, and cell types. Powered by a dose-response database, DOSE-L1000-Viz features interactive visualization, target-centric compound ranking based on efficacy and potency, and a signature search module using reference gene sets derived from generalized additive models. We benchmarked signatures derived from generalized additive models against traditional methods and demonstrated the utility of DOSE-L1000-Viz through use cases in transcription factor modulation and drug repurposing. AVAILABILITY AND IMPLEMENTATION: DOSE-L1000-Viz and the backend data are publicly accessible at: https://dosel1000.com. All code is publicly hosted on GitHub (https://github.com/JmWangBio/DOSEL1000Viz) and archived via Zenodo (https://doi.org/10.5281/zenodo.15532392).
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