Download

Click this banner to download.

eXpanda-1.0.6.tar.gz

Publication

Overview

Analysis and visualization of biological networks, such as protein-protein and protein-DNA interactions, are crucially important toward obtaining a thorough understanding of living systems. Here, we present an integrative software platform , eXpanda , which enables an analysis of a very broad range of biological networks , with a special focus on the extraction of characteristic topologies which potentially function as units in the networks. eXpanda is provided as a Perl library which gives full-automatic connections to various biological databases via a Perl programmable interface and can perform topological analysis based on graph theory. The results of these analyses are visualizable by vector graphics.

Initialization and Edit

Previously reported interactions stored in web-based databases are downloadable as a flat file via the ftp client of respective servers or is accessible through network APIs. However it is difficult to integrate them manually. By using the parsing modules of eXpanda, the interaction data are full-automatically imported to exPanda from flat files and also through APIs of the respective databases, DIP, MINT, IntAct, HPRD, MIPS, BioCyc and KEGG. The simple Interaction File format and the Graphical Markup Language file format, along with graphical attributes which the user creates using another application such as Cytoscape, are acceptable and can also be imported as eXpanda data structures. After the operations of data initialization, eXpanda may be used to edit or add further information to the data structures. The objects, such as nodes, edges or subgraphs, can be selected by the methods in the library so that the user can easily edit the information of the objects.

Analysis

In eXpanda, certain interaction scoring methods based on graph theory have been implemented, such as calculation of the degree of each node and also network motif extraction, including the extraction of cliques. A method for comparing multiple initialized datasets has also been implemented, and allows a reliability assessment of the network which the user constructs by integrating experimentally verified datasets. All of these methods will help users to characterize local topologies in the entire network and to assess their statistical significance.

Visualization

eXpanda can save the constructed or edited network as files in various formats; an SIF file, a GML file which is importable to Cytoscape, and a Scalable Vector Graphics (SVG) file as a vector image. For each node, there are 13 graphical attributes such as size, opacity, shape and label font, and seven attributes for each edge. The scores calculated by the topological analysis modules can be reflected in these attributes, such as the thickness of lines and the gradation of colors.