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Article Abstract
Summary: Understanding 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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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC12237504 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btaf353 | DOI Listing |
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