ArticleBMC bioinformatics2016
GEN3VA: aggregation and analysis of gene expression signatures from related studies.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- L2S2: chemical perturbation and CRISPR KO LINCS L1000 signature search engine.Nucleic acids research · 2025Article
- RummaGEO: Automatic mining of human and mouse gene sets from GEO.Patterns (New York, N.Y.) · 2024Article
- RummaGEO: Automatic Mining of Human and Mouse Gene Sets from GEO.bioRxiv : the preprint server for biology · 2024Article
- SigCom LINCS: data and metadata search engine for a million gene expression signatures.Nucleic acids research · 2022Article
- Article
- Protein structure-based gene expression signatures.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Connectivity Mapping Identifies BI-2536 as a Potential Drug to Treat Diabetic Kidney Disease.Diabetes · 2021Article
- The COVID-19 Drug and Gene Set Library.Patterns (New York, N.Y.) · 2020Article
- The COVID-19 Gene and Drug Set Library.Research square · 2020Article
- The RXFP3 receptor is functionally associated with cellular responses to oxidative stress and DNA damage.Aging · 2019Article
- Mining data and metadata from the gene expression omnibus.Biophysical reviews · 2019Review
- HSP90 inhibitor geldanamycin reverts IL-13- and IL-17-induced airway goblet cell metaplasia.The Journal of clinical investigation · 2019Article
- Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data.Scientific data · 2017Article
- Article
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Authors and funding
10 authors.
Funding
Abstract
backgroundGenome-wide gene expression profiling of mammalian cells is becoming a staple of many published biomedical and biological research studies. Such data is deposited into data repositories such as the Gene Expression Omnibus (GEO) for potential reuse. However, these repositories currently do not provide simple interfaces to systematically analyze collections of related studies.
resultsHere we present GENE Expression and Enrichment Vector Analyzer (GEN3VA), a web-based system that enables the integrative analysis of aggregated collections of tagged gene expression signatures identified and extracted from GEO. Each tagged collection of signatures is presented in a report that consists of heatmaps of the differentially expressed genes; principal component analysis of all signatures; enrichment analysis with several gene set libraries across all signatures, which we term enrichment vector analysis; and global mapping of small molecules that are predicted to reverse or mimic each signature in the aggregate. We demonstrate how GEN3VA can be used to identify common molecular mechanisms of aging by analyzing tagged signatures from 244 studies that compared young vs. old tissues in mammalian systems. In a second case study, we collected 86 signatures from treatment of human cells with dexamethasone, a glucocorticoid receptor (GR) agonist. Our analysis confirms consensus GR target genes and predicts potential drug mimickers.
conclusionsGEN3VA can be used to identify, aggregate, and analyze themed collections of gene expression signatures from diverse but related studies. Such integrative analyses can be used to address concerns about data reproducibility, confirm results across labs, and discover new collective knowledge by data reuse. GEN3VA is an open-source web-based system that is freely available at: http://amp.pharm.mssm.edu/gen3va .
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