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RadialTopologyViewer

Performs a graphical visualization of a bait protein interactome derived from a co-immunoprecipitation experiment. RadialTopologyViewer presents the bait as center of the interactome and all interactions identified are positioned in relative proximity to the central bait protein. In contrast to a standard network representation, the length of the edge between the central bait and the interactor can be fixed such that it reflects a property between the bait and the interactor. For example the user can choose to display the likelihood of interaction between the bait and the interactor as a function of the edge length. Moreover, interacting proteins can be grouped together in radial spokes according to a classifier like common GO term.

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RadialTopologyViewer classification

RadialTopologyViewer specifications

Software type:
Package/Module
Restrictions to use:
None
Output data:
Graphical visualization of the bait protein interactome
Programming languages:
Java
Stability:
Stable
Interface:
Graphical user interface
Input data:
A tab delimited flat file with a header, the bait, list of interactors with interaction scores and processes, additional edges between nodes
Operating system:
Unix/Linux
Computer skills:
Medium
Maintained:
Yes

RadialTopologyViewer distribution

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RadialTopologyViewer support

Maintainer

  • John R. Yates <>

Credits

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Publications

Institution(s)

Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA; Department of Physics, Albert-Ludwigs-University Freiburg, Freiburg, Germany

Funding source(s)

This work was supported by NIH grants 5R01HL079442, P01AG031097, P41 RR011823, DK075295 and HHSN268201000035C, and CFF mass spectrometry fellowship BALCH050X6.

Link to literature

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