VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology

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.

On Different Aspects of Network Analysis in Systems Biology

“…Among public network management tools that currently exist to visually explore and analyse biological networks (see review in [60]) such as Arena3D [61], GEPHI [62], igraph [63] and VisANT [64] (Table 6.2), Cytoscape [65], CellDesigner [66] and Copasi [67] are the most powerful and widely used. Cytoscape (449,030 downloads as on September 2012) is the most popular software for the visualization and analysis of interaction networks.…”

Genomics and Bioinformatics of Parkinson's Disease

“…However, an increasingly greater number of open-access databases complement the analysis of aberrant network activities from these high dimensional data (Peri et al 2003;Kanehisa et al 2004;Schaefer et al 2009). In addition, numerous tools have been developed for visually exploring and analyzing biological networks, including Cytoscape (Smoot et al 2010), VisANT (Hu et al 2009), GeneGO (http://www.genego.com/), Ingenuity (http://www.ingenuity.com/), and Pathway Studio (Nikitin et al 2003).…”

Beyond the Gene List: Exploring Transcriptomics Data in Search for Gene Function, Trait Mechanisms and Genetic Architecture

“…A large collection of these PPI databases is publicly available (see for example the Jena Protein-Protein Interaction website ppi.fli-leibniz.de/jcb_ppi_databases.html for an extensive overview). Several web-based tools can be used to analyse and visualize the PPI networks (e.g., STRING [28] and VisANT [29]). Gene lists submitted to these tools are being assembled into inter-connected networks of proteins, based on the PPI databases.…”