# DOSE-L1000-Viz: an interactive Shiny application for dose–response transcriptomic analysis, target-centric exploration, and signature search

## TL;DR

DOSE-L1000-Viz is a web tool that helps researchers explore how drugs affect gene expression across different doses and conditions.

## Contribution

It introduces an interactive platform with target-centric compound ranking and signature search using advanced modeling techniques.

## Key findings

- DOSE-L1000-Viz enables dose–response transcriptomic analysis with interactive visualization.
- Generalized additive model-derived signatures outperform traditional methods in benchmarking.
- The tool supports drug repurposing and transcription factor modulation through practical use cases.

## 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).