Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
The VisANT tool, accessible from any recent Java-enabled browser, is a platform-independent, flexible, Web-enabled program for quick and simple construction, visualization, and analysis of molecular and higher order networks based on functional (e.g., expression profiles, phylogenetic profiles) and physical (e.g., yeast two-hybrid, chromatin-immunoprecipitation) relations from either the Predictome database or user-defined data sets. Analysis capabilities include identification of feed-forward and -back loops, shortest paths, and node degree distribution. Additionally, network constructs can be saved, accessed, and shared online. VisANT is able to develop and display meta-networks for meta-nodes that are structural complexes or pathways (soon including nodes representing any kind of dense cluster). Further, VisANT supports a growing number of standard exchange formats and database referencing standards, e.g., KEGG/KGML, BioPAX (in progress), GenBank, Gene Ontology. Multiple species are supported to the extent that computed or experimental evidence of interactions or associations are available (i.e., public datasets or Predictome database).
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1002/0471250953.bi0808s08 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Using VisANT to Analyze Networks.
Curr Protoc Bioinformatics
July 2016
Bioinformatics Program, Boston University, Boston, Massachusetts.
VisANT is a Web-based workbench for the integrative analysis of biological networks with unique features such as exploratory navigation of interaction network and multi-scale visualization and inference with integrated hierarchical knowledge. It provides functionalities for convenient construction, visualization, and analysis of molecular and higher order networks based on functional (e.g.
View Article and Find Full Text PDFAnalyzing networks with VisANT.
Curr Protoc Bioinformatics
December 2004
Boston University, Boston, Massachusetts, USA.
The VisANT tool, accessible from any recent Java-enabled browser, is a platform-independent, flexible, Web-enabled program for quick and simple construction, visualization, and analysis of molecular and higher order networks based on functional (e.g., expression profiles, phylogenetic profiles) and physical (e.
View Article and Find Full Text PDFVisANT 3.0: new modules for pathway visualization, editing, prediction and construction.
Nucleic Acids Res
July 2007
Center for Advanced Genomic Technology, Boston University, Boston, MA 02215, USA.
With the integration of the KEGG and Predictome databases as well as two search engines for coexpressed genes/proteins using data sets obtained from the Stanford Microarray Database (SMD) and Gene Expression Omnibus (GEO) database, VisANT 3.0 supports exploratory pathway analysis, which includes multi-scale visualization of multiple pathways, editing and annotating pathways using a KEGG compatible visual notation and visualization of expression data in the context of pathways. Expression levels are represented either by color intensity or by nodes with an embedded expression profile.
View Article and Find Full Text PDFPredictome: a database of putative functional links between proteins.
Nucleic Acids Res
January 2002
Bioinformatics Graduate Program and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
The current deluge of genomic sequences has spawned the creation of tools capable of making sense of the data. Computational and high-throughput experimental methods for generating links between proteins have recently been emerging. These methods effectively act as hypothesis machines, allowing researchers to screen large sets of data to detect interesting patterns that can then be studied in greater detail.
View Article and Find Full Text PDF