VisANT

Category Cross-Omics>Pathway Analysis/Tools

Abstract VisANT is a software framework for visualizing, mining, analyzing and modeling multi-resolution, multi-scale biological networks and pathways.

VisANT provides gene-based integrative services to automatically resolve ambiguities that result from non-unique protein/gene notation. It is also able to integrate interaction data, splice variants (by using metagraphs), networks and pathways, thereby providing a platform to enable better modeling.

The system is highly optimized to handle large-scale networks and facilitates the fast loading of large datasets.

The unique implementation of Meta Graphs Not only enables VisANT to integrate multi-scale knowledge, but also improves network readability and system performance.

VisANT features/capabilities include:

1) Database Support -- The VisANT platform is supported by the Predictome database.

2) Interactions -- Computationally predicted 'functional associations' are produced at the Center for Advanced Genomic Technology (CAGT).

Most of the experimentally determined interaction data are collected from the Munich Information Center for Protein Sequences (MIPS) (see G6G Abstract Number 20336), Biomolecular Interaction Network Database (BIND), Human Protein Reference Database (HPRD), etc. and updated periodically.

Some large-scale experimental data, such as Chip-Chip data for transcriptional regulatory networks, is collected independently.

In addition to the computational 'predicted interactions' produced in the manufacturers Lab, the Predictome database also collects experimentally determined ones by either directly importing from literature, or by synchronizing with existing 'interaction databases' such as the Biological General Repository for Interaction Datasets (BioGRID), MIPS, BIND, HPRD, etc.

The integration of the interaction is ‘gene-based’, meaning that two (2) protein nodes will be recognized as a single protein, if the same gene encodes them.

This decision Not to distinguish gene nodes from protein nodes was based primarily on the following observations:

Because genes often encode multiple proteins, using gene id to represent both gene and protein is a natural choice; otherwise, uncertainty may arise when integrating interaction data.

3) Name Normalization and Linkout -- The Name Normalization and Linkout function in VisANT is dependent on database integration with external data sources including GenBank, SGD, Flybase, KEGG, GO, HUGO, etc.

4) Macros -- Primary support of macros to define your own work flow.

In general, macros allow users to combine tedious or repetitive tasks/analysis into one single action, making it much easier to define your own work flow, do a live demo, make a pretty network with a simple edge list, etc.

5) Batch Mode database queries -- Batch mode can automate 'database queries' for interactions and name resolutions.

You can:

6) Batch Mode batch processes -- Used to automate 'batch processes' in the background and to handle large-scale networks with millions of nodes and edges.

The batch-mode of VisANT makes it possible for VisANT to be run quietly in the background without any user interaction.

When VisANT is started in this mode, it will carry out a list of the processes specified in a command file (simply a text file).

All command files can also be directly loaded into VisANT as macros.

7) Meta-Graph [The network in which a node (meta-node) itself has an internal network structure] -- Multi-scale visualization of bio-networks, ideal for a network of 'functional modules'.

Note: A 'functional module' is a group of 'cellular components' and their interactions that can be attributed to a specific biological function.

8) Fast batch loading -- Fast batch loading of a large interaction data set through the Interaction Statistics page (see Interactions above).

9) Flexible Visual Schema of the network -- Customized node & edge annotation.

10) Integrative Data-Mining -- 405k+ 'functional associations' (Experimental: 98,924, Computational: 307,017) for 103 species, name normalization for Yeast, Fly, Homo sapiens, etc.

11) Adjustable high performance -- supports large-networks, a test has been performed with 226k+ edges and nodes.

12) Easy HTTP linking to your network and built-in support for the high resolution Scalable Vector Graph (SVG) format - so that you can convert a VisANT network into high-resolution SVG format.

13) Expression overlay of the network/pathway.

14) Integrated expression data-based recommendation system for a gene in the same pathway/complex/network.

15) Exploratory navigation of KEGG pathways.

16) Support of ‘weighted network’ using edge thickness, or edge color, or both.

17) GO browser and various options for Gene Ontology (GO) annotations.

18) VisANT has been carefully designed to fit different requirements under different scenarios.

It provides four (4) run modes as follows:

System Requirements

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Manufacturer

Manufacturer Web Site VisANT

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G6G Abstract Number 20338

G6G Manufacturer Number 100445