VisANT: an integrative framework for networks in systems biology

Abstract

The essence of a living cell is adaptation to a changing environment, and a central goal of modern cell biology is to understand adaptive change under normal and pathological conditions. Because the number of components is large, and processes and conditions are many, visual tools are useful in providing an overview of relations that would otherwise be far more difficult to assimilate. Historically, representations were static pictures, with genes and proteins represented as nodes, and known or inferred correlations between them (links) represented by various kinds of lines. The modern challenge is to capture functional hierarchies and adaptation to environmental change, and to discover pathways and processes embedded in known data, but not currently recognizable. Among the tools being developed to meet this challenge is VisANT (freely available at http://visant.bu.edu) which integrates, mines and displays hierarchical information. Challenges to integrating modeling (discrete or continuous) and simulation capabilities into such visual mining software are briefly discussed.

Histone deacetylase inhibition by Japanese encephalitis virus in monocyte/macrophages: A novel viral immune evasion strategy

“…9) that shows the possible proteinprotein interactions between the four HDACs that are currently under investigation with other proteins, both in humans and in mouse, the model of our investigation. This map has been based on a database of predicted functional associations among proteins with the help of the VisANT Project, a web-based data exploration tool (Hu et al 2008). One major function is the activation of NFB through deacetylation by HDAC3 (Hasselgren 2007).…”

Modulation of Gene Expression and Cell-Cycle Signaling Pathways by the EGFR Inhibitor Gefitinib (Iressa) in Rat Urinary Bladder Cancer

“…All network analyses were implemented in the statistical package WGCNA in R environment (18). The VisANT program was used to construct gene-gene interaction (connections) networks (19). Genes within modules were analyzed for GO term enrichment by the program DAVID (20).…”

Gene Coexpression Networks for the Analysis of DNA Microarray Data

“…Network-based methods have been applied to a wide variety of problems in biology, including the display of protein interactions [17], transcription factor binding site discovery [18], and the modeling of genetic interactions [19]. Likewise, several tools have been developed for the visualization and analysis of biological networks, including Cytoscape [20], VisAnt [21], and tYNA [22]. For a review of biological network applications, the reader is referred to [23].…”