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Osprey: a network visualization system.

Breitkreutz BJ, Stark C, Tyers M - Genome Biol. (2003)

Bottom Line: Osprey builds data-rich graphical representations that are color-coded for gene function and experimental interaction data.Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format.User-defined large-scale datasets can be readily combined with Osprey for comparison of different methods.

View Article: PubMed Central - HTML - PubMed

Affiliation: Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University Avenue, Toronto, M5G 1X5, Canada.

ABSTRACT
We have developed a software platform called Osprey for visualization and manipulation of complex interaction networks. Osprey builds data-rich graphical representations that are color-coded for gene function and experimental interaction data. Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format. User-defined large-scale datasets can be readily combined with Osprey for comparison of different methods.

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Searches and filters. (a) Network containing 2,245 vertices and 6,426 edges from combined datasets of Gavin et al. [10], shown in red, and Ho et al. [11], shown in yellow. (b) A source filter reveals only those interactions shared by both datasets, namely 212 vertices and 188 edges.
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Figure 2: Searches and filters. (a) Network containing 2,245 vertices and 6,426 edges from combined datasets of Gavin et al. [10], shown in red, and Ho et al. [11], shown in yellow. (b) A source filter reveals only those interactions shared by both datasets, namely 212 vertices and 188 edges.

Mentions: A drawback of current network visualization systems is the inability to search the network for an individual gene in the context of large graphs. To overcome this problem, Osprey allows text-search queries by gene names. A further difficulty with visualization systems is the absence of functional information within the graphical interface. This problem is remedied by Osprey, which provides a one-click link to all database fields for all displayed nodes including open reading frame (ORF) name, gene aliases, and a description of gene function. By default, this information is obtained from The GRID, which in turn compiles gene annotations provided by the Saccharomyces Genome Database (SGD [7]). Various filters have been developed that allow the user to query the network. For example, an interaction network can be parsed for interactions derived from a particular experimental method. Current Osprey filters include source, function, experimental system and connectivity (Figure 2).


Osprey: a network visualization system.

Breitkreutz BJ, Stark C, Tyers M - Genome Biol. (2003)

Searches and filters. (a) Network containing 2,245 vertices and 6,426 edges from combined datasets of Gavin et al. [10], shown in red, and Ho et al. [11], shown in yellow. (b) A source filter reveals only those interactions shared by both datasets, namely 212 vertices and 188 edges.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC153462&req=5

Figure 2: Searches and filters. (a) Network containing 2,245 vertices and 6,426 edges from combined datasets of Gavin et al. [10], shown in red, and Ho et al. [11], shown in yellow. (b) A source filter reveals only those interactions shared by both datasets, namely 212 vertices and 188 edges.
Mentions: A drawback of current network visualization systems is the inability to search the network for an individual gene in the context of large graphs. To overcome this problem, Osprey allows text-search queries by gene names. A further difficulty with visualization systems is the absence of functional information within the graphical interface. This problem is remedied by Osprey, which provides a one-click link to all database fields for all displayed nodes including open reading frame (ORF) name, gene aliases, and a description of gene function. By default, this information is obtained from The GRID, which in turn compiles gene annotations provided by the Saccharomyces Genome Database (SGD [7]). Various filters have been developed that allow the user to query the network. For example, an interaction network can be parsed for interactions derived from a particular experimental method. Current Osprey filters include source, function, experimental system and connectivity (Figure 2).

Bottom Line: Osprey builds data-rich graphical representations that are color-coded for gene function and experimental interaction data.Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format.User-defined large-scale datasets can be readily combined with Osprey for comparison of different methods.

View Article: PubMed Central - HTML - PubMed

Affiliation: Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University Avenue, Toronto, M5G 1X5, Canada.

ABSTRACT
We have developed a software platform called Osprey for visualization and manipulation of complex interaction networks. Osprey builds data-rich graphical representations that are color-coded for gene function and experimental interaction data. Mouse-over functions allow rapid elaboration and organization of network diagrams in a spoke model format. User-defined large-scale datasets can be readily combined with Osprey for comparison of different methods.

Show MeSH