ArticleNucleic acids research2009
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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Who cites it
86 citing papers in PubMed.
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- NORMA: The Network Makeup Artist - A Web Tool for Network Annotation Visualization.Genomics, proteomics & bioinformatics · 2022Article
- Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review.Biomolecules · 2021Review
- Tracing the footsteps of autophagy in computational biology.Briefings in bioinformatics · 2021Article
- Mapping the multiscale structure of biological systems.Cell systems · 2021Review
- A Guide to Conquer the Biological Network Era Using Graph Theory.Frontiers in bioengineering and biotechnology · 2020Review
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- NIPS, a 3D network-integrated predictor of deleterious protein SAPs, and its application in cancer prognosis.Scientific reports · 2018Article
- Bipartite graphs in systems biology and medicine: a survey of methods and applications.GigaScience · 2018Review
- Identification of candidate genes related to pancreatic cancer based on analysis of gene co-expression and protein-protein interaction network.Oncotarget · 2017Article
- Methods, Tools and Current Perspectives in Proteogenomics.Molecular & cellular proteomics : MCP · 2017Review
- Weighted gene co-expression network analysis of gene modules for the prognosis of esophageal cancer.Journal of Huazhong University of Science and Technology. Medical sciences = Hua zhong ke ji da xue xue bao. Yi xue Ying De wen ban = Huazhong keji daxue xuebao. Yixue Yingdewen ban · 2017Article
- Computational dynamic approaches for temporal omics data with applications to systems medicine.BioData mining · 2017Review
- Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis.Advances in bioinformatics · 2017Review
- Undiscovered Physiology of Transcript and Protein Networks.Comprehensive Physiology · 2016Review
- Algorithms for modeling global and context-specific functional relationship networks.Briefings in bioinformatics · 2016Article
- Identification of breast cancer candidate genes using gene co-expression and protein-protein interaction information.Oncotarget · 2016Article
- Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.PLoS computational biology · 2016Article
- KnowEnG: a knowledge engine for genomics.Journal of the American Medical Informatics Association : JAMIA · 2015Article
26 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
Despite its wide usage in biological databases and applications, the role of the gene ontology (GO) in network analysis is usually limited to functional annotation of genes or gene sets with auxiliary information on correlations ignored. Here, we report on new capabilities of VisANT--an integrative software platform for the visualization, mining, analysis and modeling of the biological networks--which extend the application of GO in network visualization, analysis and inference. The new VisANT functions can be classified into three categories. (i) Visualization: a new tree-based browser allows visualization of GO hierarchies. GO terms can be easily dropped into the network to group genes annotated under the term, thereby integrating the hierarchical ontology with the network. This facilitates multi-scale visualization and analysis. (ii) Flexible annotation schema: in addition to conventional methods for annotating network nodes with the most specific functional descriptions available, VisANT also provides functions to annotate genes at any customized level of abstraction. (iii) Finding over-represented GO terms and expression-enriched GO modules: two new algorithms have been implemented as VisANT plugins. One detects over-represented GO annotations in any given sub-network and the other finds the GO categories that are enriched in a specified phenotype or perturbed dataset. Both algorithms take account of network topology (i.e. correlations between genes based on various sources of evidence). VisANT is freely available at http://visant.bu.edu.
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