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Visualisation of BioPAX Networks using BioLayout Express (3D).

Published version
Peer-reviewed

Type

Article

Change log

Authors

Wright, Derek W 
Angus, Tim 
Enright, Anton J 
Freeman, Tom C 

Abstract

BioLayout Express (3D) is a network analysis tool designed for the visualisation and analysis of graphs derived from biological data. It has proved to be powerful in the analysis of gene expression data, biological pathways and in a range of other applications. In version 3.2 of the tool we have introduced the ability to import, merge and display pathways and protein interaction networks available in the BioPAX Level 3 standard exchange format. A graphical interface allows users to search for pathways or interaction data stored in the Pathway Commons database. Queries using either gene/protein or pathway names are made via the cPath2 client and users can also define the source and/or species of information that they wish to examine. Data matching a query are listed and individual records may be viewed in isolation or merged using an 'Advanced' query tab. A visualisation scheme has been defined by mapping BioPAX entity types to a range of glyphs. Graphs of these data can be viewed and explored within BioLayout as 2D or 3D graph layouts, where they can be edited and/or exported for visualisation and editing within other tools.

Description

Keywords

signalling network, analysis, proteins, bioinformatics

Journal Title

F1000Res

Conference Name

Journal ISSN

2046-1402
1759-796X

Volume Title

3

Publisher

F1000 Research Ltd