Tool for pathway visualization, editing, prediction and construction.
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.