ArticleBMC bioinformatics2019
FunSet: an open-source software and web server for performing and displaying Gene Ontology enrichment analysis.
Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
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- vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis.BMC bioinformatics · 2024Article
- Claudin-2 protects against colitis-associated cancer by promoting colitis-associated mucosal healing.The Journal of clinical investigation · 2023Article
- Empowering biologists to decode omics data: the Genekitr R package and web server.BMC bioinformatics · 2023Article
- T-cell trans-synaptic vesicles are distinct and carry greater effector content than constitutive extracellular vesicles.Nature communications · 2022Article
- MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses.Genetics · 2022Article
- A Four-Gene Signature Associated with Radioresistance in Head and Neck Squamous Cell Carcinoma Identified by Text Mining and Data Analysis.Computational and mathematical methods in medicine · 2022Article
- GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data.BMC bioinformatics · 2021Article
- MiR-212-3p functions as a tumor suppressor gene in group 3 medulloblastoma via targeting nuclear factor I/B (NFIB).Acta neuropathologica communications · 2021Article
- Genome-Wide Association Study on Reproduction-Related Body-Shape Traits of Chinese Holstein Cows.Animals : an open access journal from MDPI · 2021Article
- Computational screening of potential glioma-related genes and drugs based on analysis of GEO dataset and text mining.PloS one · 2021Article
- Development of an Immune-Related Prognostic Index Associated With Glioblastoma.Frontiers in neurology · 2021Article
- AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species.BMC bioinformatics · 2020Article
- Comprehensive analysis reveals a four-gene signature in colorectal cancer.Translational cancer research · 2020Article
- Presence and structure-activity relationship of intrinsically disordered regions across mucins.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2020Article
- Uncovering and characterizing splice variants associated with survival in lung cancer patients.PLoS computational biology · 2019Article
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3 authors.
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Abstract
backgroundGene Ontology enrichment analysis provides an effective way to extract meaningful information from complex biological datasets. By identifying terms that are significantly overrepresented in a gene set, researchers can uncover biological features shared by genes. In addition to extracting enriched terms, it is also important to visualize the results in a way that is conducive to biological interpretation.
resultsHere we present FunSet, a new web server to perform and visualize enrichment analysis. The web server identifies Gene Ontology terms that are statistically overrepresented in a target set with respect to a background set. The enriched terms are displayed in a 2D plot that captures the semantic similarity between terms, with the option to cluster terms via spectral clustering and identify a representative term for each cluster. FunSet can be used interactively or programmatically, and allows users to download the enrichment results both in tabular form and in graphical form as SVG files or in data format as JSON or csv. To enhance reproducibility of the analyses, users have access to historical data for the ontology and the annotations. The source code for the standalone program and the web server are made available with an open-source license.
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