DOSE-L1000-Viz: an interactive Shiny application for dose-response transcriptomic analysis, target-centric exploration, and signature search.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 40608961.
- Also identified by DOI 10.1093/bioinformatics/btaf353 and PMC identifier 12237504.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. 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).
Medical subject headings
- Gene Expression Profiling
- Software
- Transcriptome