ArticleNucleic acids research2020
signatureSearch: environment for gene expression signature searching and functional interpretation.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Foxs1-mediated transformation of CD34EMBO molecular medicine · 2026Article
- Gene expression profiling of whole blood samples following marathon running in non-elite athletes.Biology of sport · 2026Article
- Aging rate indicators and the search for anti-aging drugs.Frontiers in science · 2026Article
- Single-cell multi-omics analysis reveals cancer regulatory elements of transcriptional programs and clinical implications.Cell death & disease · 2025Article
- L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine.Nucleic acids research · 2025Article
- DOSE-L1000-Viz: an interactive Shiny application for dose-response transcriptomic analysis, target-centric exploration, and signature search.Bioinformatics (Oxford, England) · 2025Article
- Integrative transcriptome-based drug repurposing in tuberculosis.bioRxiv : the preprint server for biology · 2025Article
- Cell type and region-specific transcriptional changes in the endometrium of women with RIF identify potential treatment targets.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- GSFM: A genome-scale functional module transformation to represent drug efficacy forActa pharmaceutica Sinica. B · 2025Article
- WebCMap: an R package for high-throughput connectivity analysis within the CMap framework.Bioinformatics advances · 2025Article
- The lifespan-extending MEK1 inhibitor trametinib promotes regulation of de novo lipogenesis enzymes by chaperone-mediated autophagy.Frontiers in aging · 2025Article
- Mechanism-free repurposing of drugs for C9orf72-related ALS/FTD using large-scale genomic data.Cell genomics · 2024Article
- Transcriptomic Analyses Predict Enhanced Metabolic Activity and Therapeutic Potential of mTOR Inhibitors in Acne-Prone Skin.JID innovations : skin science from molecules to population health · 2024Article
- SuperFeat: Quantitative Feature Learning from Single-cell RNA-seq Data Facilitates Drug Repurposing.Genomics, proteomics & bioinformatics · 2024Article
- Signature Search Polestar: a comprehensive drug repurposing method evaluation assistant for customized oncogenic signature.Bioinformatics (Oxford, England) · 2024Article
- Article
- Signature reversion of three disease-associated gene signatures prioritizes cancer drug repurposing candidates.FEBS open bio · 2024Article
- A network-based drug prioritization and combination analysis for the MEK5/ERK5 pathway in breast cancer.BioData mining · 2024Article
- Unraveling athletic performance: Transcriptomics and external load monitoring in handball competition.PloS one · 2024Article
- Prioritized polycystic kidney disease drug targets and repurposing candidates from pre-cystic and cystic mouse Pkd2 model gene expression reversion.Molecular medicine (Cambridge, Mass.) · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
signatureSearch is an R/Bioconductor package that integrates a suite of existing and novel algorithms into an analysis environment for gene expression signature (GES) searching combined with functional enrichment analysis (FEA) and visualization methods to facilitate the interpretation of the search results. In a typical GES search (GESS), a query GES is searched against a database of GESs obtained from large numbers of measurements, such as different genetic backgrounds, disease states and drug perturbations. Database matches sharing correlated signatures with the query indicate related cellular responses frequently governed by connected mechanisms, such as drugs mimicking the expression responses of a disease. To identify which processes are predominantly modulated in the GESS results, we developed specialized FEA methods combined with drug-target network visualization tools. The provided analysis tools are useful for studying the effects of genetic, chemical and environmental perturbations on biological systems, as well as searching single cell GES databases to identify novel network connections or cell types. The signatureSearch software is unique in that it provides access to an integrated environment for GESS/FEA routines that includes several novel search and enrichment methods, efficient data structures, and access to pre-built GES databases, and allowing users to work with custom databases.
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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.