VisANT is a three-tier
enterprise system designed specifically for the integrative visual
data-mining of multi-scale Bio-Network/Pathways. It features:
Network Module Enrichment
Analysis (NMEA) to detect phenotypic difference between two
data sets (e.g. gene expression of disease v.s. normal), try
NMEA for cell cycle pathway in P53 mutant data. NMEA is deigned to
find functional modules that inform phenotypic differences. For the
current release, such differences are usually transcriptional
activity. NMEA by default will be performed for all non-embedded
metanodes. The function is available under the
menu and requires the input of expression data (sample
expression data). When execution of NMEA is complete, the nodes in
the modules will be colored according to their enrichment scores
GO Term Enrichment Analysis (GOTEA) to
find the over-represented GO terms in network modules.
The function is available under the
menu and requires genes in the modules being annotated. A quick
can be tried here. An example with
the step-by-step macros is
illustrated here to predict the function of KEGG cell cycle
pathway using both hyper-geometry test and GOTEA.
The macro file can be downloaded here.
each step is explained in detail in the comments.
automates database queries for interactions, name resolutions, and GO
to automate batch processes in the background and to handle
large-scale networks with millions nodes and edges.
A test case has been carried out
15,447 nodes and 1,722,708 edges as shown below,
information can be found here
Flexible Visual Schema of the network:
Customized node&edge annotation,
Screenshot |Sample Network
Integrative Data-Mining: 405k+ functional
associations (Experimental:98924, Computational:307017) for 103
species, name normalization for Yeast, Fly, Homo sapiens etc.,
Adjustable high performance, supports
large-network, test has been performed with 226k+ edges and
http linking to your network and
built-in support of high resolution SVG,
sample http linking.....
Expression overlay of the network/pathway
Integrated expression data-based
recommendation system for gene in the same pathway/complex/network
Exploratory navigation of KEGG pathways.
Support of weighted network using edge
thickness, or edge color , or both.