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Analyzing Networks with VisANT
Publication Name:
Current Protocols in Bioinformatics
Unit Number:
Unit 8.8
DOI:
10.1002/0471250953.bi0808s08
Online Posting Date:
December, 2004 Abstract
The VisANT tool, accessible from any recent Java-enabled browser, is a platform-independent, flexible, Web-enabled program for quick and simple construction, visualization, and analysis of molecular and higher order networks based on functional (e.g., expression profiles, phylogenetic profiles) and physical (e.g., yeast two-hybrid, chromatin-immunoprecipitation) relations from either the Predictome database or user-defined data sets. Analysis capabilities include identification of feed-forward and -back loops, shortest paths, and node degree distribution. Additionally, network constructs can be saved, accessed, and shared online. VisANT is able to develop and display meta-networks for meta-nodes that are structural complexes or pathways (soon including nodes representing any kind of dense cluster). Further, VisANT supports a growing number of standard exchange formats and database referencing standards, e.g., KEGG/KGML, BioPAX (in progress), GenBank, Gene Ontology. Multiple species are supported to the extent that computed or experimental evidence of interactions or associations are available (i.e., public datasets or Predictome database).
Keywords: interaction; network; meta-network; visualization; integration
Table of Contents
- Unit Introduction
- Basic Protocol 1: Basic Network Construction
- Alternate Protocol: Constructing and Comparing Large-Scale Networks
- Support Protocol 1: Quantitative Characteristics of Network Topologies
- Support Protocol 2: Online Saving and Reading of the Network
- Basic Protocol 2: Analyzing the Biological Network
- Basic Protocol 3: Meta-Networks: An Application to Protein Complexes
- Commentary
- Literature Cited
- Figures
Figures
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Figure 8.8.1Relationships between protocols. Protocols are colored by type, with the direction of the line indicating relationship—for example, the -
Figure 8.8.2The VisANT start page. -
Figure 8.8.3VisANT main window. -
Figure 8.8.4Methods table. -
Figure 8.8.5Searching interactions of FUS1 and STE3 proteins. The circles represent genes or proteins, depending on the assay by which the relations were obtained; the connecting lines (links) represent relations established by the selected methods. The methods table can be viewed by clicking on the View menu in the menu bar. A minus sign (–) in the node indicates that the interaction has been expanded (i.e., all links are shown) while a plus symbol (+) indicates that links remain hidden. -
Figure 8.8.6The difference between three spring-forces-based layout algorithms. -
Figure 8.8.7The result after invoking a relaxation algorithm. In this case the Elegant Relaxation algorithm was used (see descriptions below). -
Figure 8.8.8How to select all the nodes in the network panel. Note that selected nodes are clearly marked on the screen. -
Figure 8.8.9Querying all the nodes in the network panel. -
Figure 8.8.10A low resolution view of the network that contains STE3 and FUS1. -
Figure 8.8.11Shortest paths between STE3 and FUS1. -
Figure 8.8.12PPI network (yeast two hybrid) of S. cerevisiae. -
Figure 8.8.13Combined network of PPI (blue region) and genetic network (green) for S. cerevisiae. -
Figure 8.8.14Status report of the combined network -
Figure 8.8.15The intersection of the combined network. Each edge is labeled with two colors, indicating that the association is obtained by two methods. -
Figure 8.8.16Degree distribution of regulatory network (ChIP). -
Figure 8.8.17Feedback loop retrieved from a complex transcription-factor/target network. -
Figure 8.8.18An example of shortest path detection. -
Figure 8.8.19The network of physical interactions within which STE3 and FUS1 are embedded. -
Figure 8.8.20Network after collapse of a set of nodes. -
Figure 8.8.21The pruned physical interaction network containing FUS1 and STE3. -
Figure 8.8.22Node Properties window. -
Figure 8.8.23Network with annotated shortest path between FUS1 and STE3. -
Figure 8.8.24Adding node annotation from a linked data source. -
Figure 8.8.25Integration of different data sources. Complexes (meta-nodes) were determined by tandem affinity mass spectrometry (Gavin et al., -
Figure 8.8.26Degree distribution of complex network: the power-law does not hold.
Literature Cited
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| Bader, G.D., Betel, D., and Hogue, C.W. 2003. BIND: The Biomolecular Interaction Network Database. Nucleic Acids Res. 31:248-250. | |
| Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Wheeler, D.L. 2003. GenBank. Nucleic Acids Res. 31:23-27. | |
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| Yu, J., Smith, V.A., Wang, P.P., Hartemink, A.J., and Jarvis, E.D. 2004. Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics. [available online ahead of print at http://bioinformatics.oupjournals.org/cgi/reprint/bth448v1] | |
| Yanai, I. and DeLisi, C. 2002. The society of genes: Networks of functional links between genes from comparative genomics. Genome Biol. 25:research0064. [Epub at http://www.pubmedcentral.nih.gov/articlerender.fcgi tool=pubmed&pubmedid=12429063] | |
| Key References | |
| Hu, Z., Mellor, J., Wu, J., DeLisi, C. 2004. VisANT: An online visualization and analysis tool for biological interaction data. BMC Bioinformatics 5:17. | |
| Explains the design principals and future development of VisANT. | |
| Mellor et al., 2002. See | |
| Introduces the development of Predictome database. | |
| Internet Resources | |
| http://visant.bu.edu | |
| VisANT homepage. | |
| http://visant.bu.edu/vmanual | |
| The VisANT user's manual. | |
| http://predictome.bu.edu | |
| Homepage for the Predictome database | |
| http://java.sun.com | |
| Free source of Java run-time environment 1.4 or above. Refer to VisANT user manual for detailed instruction. | |
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