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
Literature & Tutorials:
PubMed Link: VisANT -- data-integrating visual framework for biological networks and modules
-- 2007 Update: VisANT 3.0: new modules for pathway visualization, editing, prediction and construction
-- 2009 Update -- VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
-- 2007 Update: VisANT 3.0: new modules for pathway visualization, editing, prediction and construction
-- 2009 Update -- VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology
This record last updated: 09-03-2009