Analyzing Networks with VisANT
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- Abstract
- Table of Contents
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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
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PDF or HTML at Wiley Online LibraryTable of Contents
- Basic Protocol 1: Basic Network Construction
- Alternate Protocol 1: 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
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Figure 8.8.1 Relationships between protocols. Protocols are colored by type, with the direction of the line indicating relationship—for example, the is used by and . To distinguish the relationships of the Support Protocols, dashed lines are used for . View Image -
Figure 8.8.2 The VisANT start page. View Image -
Figure 8.8.3 VisANT main window. View Image -
Figure 8.8.4 Methods table. View Image -
Figure 8.8.5 Searching 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. View Image -
Figure 8.8.6 The difference between three spring‐forces‐based layout algorithms. View Image -
Figure 8.8.7 The result after invoking a relaxation algorithm. In this case the Elegant Relaxation algorithm was used (see descriptions below). View Image -
Figure 8.8.8 How to select all the nodes in the network panel. Note that selected nodes are clearly marked on the screen. View Image -
Figure 8.8.9 Querying all the nodes in the network panel. View Image -
Figure 8.8.10 A low resolution view of the network that contains STE3 and FUS1. View Image -
Figure 8.8.11 Shortest paths between STE3 and FUS1. View Image -
Figure 8.8.12 PPI network (yeast two hybrid) of S. cerevisiae . View Image -
Figure 8.8.13 Combined network of PPI (blue region) and genetic network (green) for S. cerevisiae . View Image -
Figure 8.8.14 Status report of the combined network View Image -
Figure 8.8.15 The intersection of the combined network. Each edge is labeled with two colors, indicating that the association is obtained by two methods. View Image -
Figure 8.8.16 Degree distribution of regulatory network (ChIP). View Image -
Figure 8.8.17 Feedback loop retrieved from a complex transcription‐factor/target network. View Image -
Figure 8.8.18 An example of shortest path detection. View Image -
Figure 8.8.19 The network of physical interactions within which STE3 and FUS1 are embedded. View Image -
Figure 8.8.20 Network after collapse of a set of nodes. View Image -
Figure 8.8.21 The pruned physical interaction network containing FUS1 and STE3. View Image -
Figure 8.8.22 Node Properties window. View Image -
Figure 8.8.23 Network with annotated shortest path between FUS1 and STE3. View Image -
Figure 8.8.24 Adding node annotation from a linked data source. View Image -
Figure 8.8.25 Integration of different data sources. Complexes (meta‐nodes) were determined by tandem affinity mass spectrometry (Gavin et al., ); the internal connections were determined by a variety of methods as indicated. (A ) Network of protein complex after it has been laid out. The rectangle represents the region of interest for zoom‐in. (B ) The region of interest of the network after zoom‐in, with several complexes labeled according to its original reference. (C ) Internal network structure of Complex 153 after integration with the interaction data from the Predictome database. All nodes are connected. (D ) Internal network structure of Complex 175 after integration with the data from Predictome database. View Image -
Figure 8.8.26 Degree distribution of complex network: the power‐law does not hold. View Image
Videos
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| 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 above. | |
| 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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