Visualisation of BioPAX Networks using BioLayout Express (3D)

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.

Keywords: signalling network, analysis, proteins, bioinformatics.

Figure 1.. Import Network user interfaces with main features highlighted.

( A) Import Network search dialog. This dialog supports the querying of the Pathway Commons database. 1. Keywords are entered into the Keywords field. To restrict the search to the BioPAX pathway name only (as opposed to all text associated with pathway), leave the ‘Name’ checkbox ticked. Terms may be separated with Boolean operators AND/OR and a specific search field may be combined with a search term separated by a colon (:) and wildcards may be searched using an asterisk (*); 2. NCBI organism ID number or species name may be entered in the text field or for convenience popular species may be searched for using the checkboxes provided; 3. Information from specific databases from which Pathway Commons aggregates may be selected, restricting searches to information provided by those resources; 4. Dropdown list defines which BioPAX type to search for: Pathway, Interaction, Physical Entity, Entity Reference. There is an additional option, Top Pathways, which is a special case; this is defined as “pathways that are neither ‘controlled’ nor ‘pathwayComponent’ of another process”; 5. Click the Search button to perform the search. Search results are displayed in the table. Results are returned in pages of 500 search hits; the sequence of pages may be navigated using the Next/ Previous buttons; 6. Click on a row in the results table to display detailed information about that network in the pane on the right hand side; 7. Click the Open button to download and display the network for the search hit you have highlighted in the results table; 8. If you wish to perform an advanced graph query, double-click the row(s) in the results table and the search hits will be added to the Advanced tab. The Advanced tab of the Import Network dialog enables you to perform advanced graph queries on search merging networks etc.; 9. When the procedure is defined, click Execute to visualise the results.

Figure 2.. Table listing BioPAX concepts and the mapping on to the mEPN pathway notation scheme and their representation in BioLayout Express ^3D as 2D and 3D nodes.

Figure 3.. Visualisation of BioPAX networks in BioLayout Express ^3D.

( A) 3D network view of a BioPAX query. Different entity/concept types defined in BioPAX Level 3 are translated into nodes of different size, shape and colour depending on type. Graphs may be explored, edited and names displayed. Options for these functionalities are contained within the BioLayout menus. ( B) The names and node types of selected nodes may be viewed with the Class Viewer, which also provides information on the number of edges. Within this window nodes may be selected/deselected, searched by name or class and information exported.