ArticleNucleic acids research2025
L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- MondrianMap: Navigating Gene Set Hierarchies with Multi-Resolution Enrichment Maps.bioRxiv : the preprint server for biology · 2026Article
- ExPO: an exposure-conditioned neural operator for L1000 signature prediction.Journal of cheminformatics · 2026Article
- The deubiquitinase activity of CYLD is required for B cell differentiation.Cell death & disease · 2026Article
- Transcriptomic data and biomedical literature synergize in finding pharmacologic gene regulators.bioRxiv : the preprint server for biology · 2026Article
- From Regeneration Failure to Functional Restoration: Unlocking the Neuronal-Intrinsic Regenerative Capacity as a Therapeutic Frontier for Optic Neuropathy and Glaucoma.CNS neuroscience & therapeutics · 2026Review
- Clusterin expression and germinal center morphometry help distinguish idiopathic multicentric castleman disease from select lymphadenopathies.Frontiers in immunology · 2026Article
- Cell-type-agnostic differential gene expression uncovers conserved principles of cellular regulation.bioRxiv : the preprint server for biology · 2025Article
- DOSE-L1000-Viz: an interactive Shiny application for dose-response transcriptomic analysis, target-centric exploration, and signature search.Bioinformatics (Oxford, England) · 2025Article
- WebCMap: an R package for high-throughput connectivity analysis within the CMap framework.Bioinformatics advances · 2025Article
- sc2DAT: workflow for targeting tumor subpopulations of single cells.Bioinformatics advances · 2025Article
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Authors and funding
4 authors.
Funding
Abstract
As part of the Library of Integrated Network-Based Cellular Signatures (LINCS) NIH initiative, 248 human cell lines were profiled with the L1000 assay to measure the effect of 33 621 small molecules and 7508 single-gene CRISPR knockouts. From this massive dataset, we computed 1.678 million sets of up- and down-regulated genes. These gene sets are served for search by the LINCS L1000 Signature Search (L2S2) web server application. With L2S2, users can identify small molecules and single gene CRISPR KOs that produce gene expression profiles similar or opposite to their submitted single or up/down gene sets. L2S2 also includes a consensus search feature that ranks perturbations across all cellular contexts, time points, and concentrations. To demonstrate the utility of L2S2, we crossed the L2S2 gene sets with gene sets collected for the RummaGEO resource. The analysis identified clusters of differentially expressed genes that match drug classes, tissues, and diseases, pointing to many opportunities for drug repurposing and drug discovery. Overall, the L2S2 web server application can be used to further the development of personalized therapeutics while expanding our understanding of complex human diseases. The L2S2 web server application is available at https://l2s2.maayanlab.cloud.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.