VisANT -- Integrative Visual Analysis Tool for Biological Networks and Pathways

What you can do:
Tool for pathway visualization, editing, prediction and construction.
Highlights:
  • 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.
  • Multiple experiments can be navigated or animated.
  • Known KEGG pathways can be enriched by querying either coexpressed components of known pathway members or proteins with known physical interactions.
  • Predicted pathways for genes/proteins with unknown functions can be inferred from coexpression or physical interaction data.
  • Pathways produced in VisANT can be saved as computer-readable XML format (VisML), graphic images or high-resolution Scalable Vector Graphics (SVG).
  • Pathways in the format of VisML can be securely shared within an interested group or published online using a simple Web link.
  • A new tree-based browser allows visualization of GO hierarchies.
  • 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.
  • 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.
Keywords:
  • biological interactions
  • biomolecular interactions
  • cellular pathway analysis tool
  • metabolic pathway analysis tool
  • gene expression regulation pathway analysis tool
  • protein interaction mapping
  • protein-protein interactions
  • signal transduction pathways
  • gene expression profiling
This record last updated: 09-03-2009
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