ArticleBMC bioinformatics2017
NaviGO: interactive tool for visualization and functional similarity and coherence analysis with gene ontology.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- GO2Sum: generating human-readable functional summary of proteins from GO terms.NPJ systems biology and applications · 2024Article
- PRRGO: A Tool for Visualizing and Mapping Globally Expressed Genes in Public Gene Expression Omnibus RNA-Sequencing Studies to PageRank-scored Gene Ontology Terms.bioRxiv : the preprint server for biology · 2024Article
- GOTermViewer: Visualization of Gene Ontology Enrichment in Multiple Differential Gene Expression Analyses.Bioinformatics and biology insights · 2024Article
- Domain-PFP allows protein function prediction using function-aware domain embedding representations.Communications biology · 2023Article
- Domain-PFP: Protein Function Prediction Using Function-Aware Domain Embedding Representations.bioRxiv : the preprint server for biology · 2023Article
- Pan-Cancer Analysis Reveals Functional Similarity of Three lncRNAs across Multiple Tumors.International journal of molecular sciences · 2023Article
- PRO-Simat: Protein network simulation and design tool.Computational and structural biotechnology journal · 2023Article
- The First Pituitary Proteome Landscape From Matched Anterior and Posterior Lobes for a Better Understanding of the Pituitary Gland.Molecular & cellular proteomics : MCP · 2023Article
- metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data.GigaScience · 2022Article
- Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana.The ISME journal · 2022Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe number of genomics and proteomics experiments is growing rapidly, producing an ever-increasing amount of data that are awaiting functional interpretation. A number of function prediction algorithms were developed and improved to enable fast and automatic function annotation. With the well-defined structure and manual curation, Gene Ontology (GO) is the most frequently used vocabulary for representing gene functions. To understand relationship and similarity between GO annotations of genes, it is important to have a convenient pipeline that quantifies and visualizes the GO function analyses in a systematic fashion.
resultsNaviGO is a web-based tool for interactive visualization, retrieval, and computation of functional similarity and associations of GO terms and genes. Similarity of GO terms and gene functions is quantified with six different scores including protein-protein interaction and context based association scores we have developed in our previous works. Interactive navigation of the GO function space provides intuitive and effective real-time visualization of functional groupings of GO terms and genes as well as statistical analysis of enriched functions.
conclusionsWe developed NaviGO, which visualizes and analyses functional similarity and associations of GO terms and genes. The NaviGO webserver is freely available at: http://kiharalab.org/web/navigo .
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