VisANT: an online visualization and analysis tool for biological interaction data - PubMed (original) (raw)

Comparative Study

VisANT: an online visualization and analysis tool for biological interaction data

Zhenjun Hu et al. BMC Bioinformatics. 2004.

Abstract

Background: New techniques for determining relationships between biomolecules of all types--genes, proteins, noncoding DNA, metabolites and small molecules--are now making a substantial contribution to the widely discussed explosion of facts about the cell. The data generated by these techniques promote a picture of the cell as an interconnected information network, with molecular components linked with one another in topologies that can encode and represent many features of cellular function. This networked view of biology brings the potential for systematic understanding of living molecular systems.

Results: We present VisANT, an application for integrating biomolecular interaction data into a cohesive, graphical interface. This software features a multi-tiered architecture for data flexibility, separating back-end modules for data retrieval from a front-end visualization and analysis package. VisANT is a freely available, open-source tool for researchers, and offers an online interface for a large range of published data sets on biomolecular interactions, including those entered by users. This system is integrated with standard databases for organized annotation, including GenBank, KEGG and SwissProt. VisANT is a Java-based, platform-independent tool suitable for a wide range of biological applications, including studies of pathways, gene regulation and systems biology.

Conclusion: VisANT has been developed to provide interactive visual mining of biological interaction data sets. The new software provides a general tool for mining and visualizing such data in the context of sequence, pathway, structure, and associated annotations. Interaction and predicted association data can be combined, overlaid, manipulated and analyzed using a variety of built-in functions. VisANT is available at http://visant.bu.edu.

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Figures

Figure 1

Sample view of a VisAnt application. Displayed are connections in a segment of the MAPK regulatory network constructed by data from Lee et. al.,[29] (Brown lines with arrows, indicating binding of protein to DNA) and correlations in microarray experiments published by Hughes, et al[30] (green lines), as well as links established by protein-protein binding etc. Genes for membrane-bound receptors, and related pathway proteins and transcription factors linked by physical interaction and gene expression relation are shown. Protein/DNA is represented as the nodes. Red nodes represent proteins that are annotated in at least one KEGG pathway (the quick-tip of node STE12 indicates that it maps to KEGG pathway 04010). A "-" indicates that the node is fully expanded (i.e. all connections are shown) while the "+" indicates that some links have not yet been displayed. Correlations between nodal proteins are indicated by connecting lines (edges), different colors corresponding to different experimental methods.

Figure 2

Illustration of data integration in VisANT. (A) The MAPK related network constructed from receptors and transcription factors in the pheromone-response pathway. Purple rectangles demonstrate the quick-tip obtained by mouse-overs of the edge between DIG1 and FUS3, and the nodes CHA3 and STE12 respectively. Most integration data are available only after the node has been queried against the databases, and are available under the "Available Links" submenu of the node. (B) GenBank[37] record of human homology protein for CHA1 based on COG database. The homology information is available after the corresponding filter has been processed. (C) STE12 is mapped to KEGG pathway 04010 (MAPK Singling Pathway) and the pathway has been loaded with corresponding nodes highlighted. (D) Functional annotation of STE5 is loaded through the cross-reference in SGD[49] database.

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VisANT: an online visualization and analysis tool for biological interaction data - PubMed (original) (raw)