Dataset Information

Interactive, multiscale navigation of large and complicated biological networks.

ABSTRACT:

Motivation

Many types of omics data are compiled as lists of connections between elements and visualized as networks or graphs where the nodes and edges correspond to the elements and the connections, respectively. However, these networks often appear as 'hair-balls'-with a large number of extremely tangled edges-and cannot be visually interpreted.

Results

We present an interactive, multiscale navigation method for biological networks. Our approach can automatically and rapidly abstract any portion of a large network of interest to an immediately interpretable extent. The method is based on an ultrafast graph clustering technique that abstracts networks of about 100 000 nodes in a second by iteratively grouping densely connected portions and a biological-property-based clustering technique that takes advantage of biological information often provided for biological entities (e.g. Gene Ontology terms). It was confirmed to be effective by applying it to real yeast protein network data, and would greatly help modern biologists faced with large, complicated networks in a similar manner to how Web mapping services enable interactive multiscale navigation of geographical maps (e.g. Google Maps).

Availability

Java implementation of our method, named NaviCluster, is available at http://navicluster.cb.k.u-tokyo.ac.jp/.

Contact

thanet@cb.k.u-tokyo.ac.jp

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Praneenararat T

PROVIDER: S-EPMC3072549 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Interactive, multiscale navigation of large and complicated biological networks.

Praneenararat Thanet T Takagi Toshihisa T Iwasaki Wataru W

Bioinformatics (Oxford, England) 20110223 8

<h4>Motivation</h4>Many types of omics data are compiled as lists of connections between elements and visualized as networks or graphs where the nodes and edges correspond to the elements and the connections, respectively. However, these networks often appear as 'hair-balls'-with a large number of extremely tangled edges-and cannot be visually interpreted.<h4>Results</h4>We present an interactive, multiscale navigation method for biological networks. Our approach can automatically and rapidly ab ...[more]

PMID: 21349867

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Project description:BackgroundLinking high-throughput experimental data with biological networks is a key step for understanding complex biological systems. Currently, visualization tools for large metabolic networks often result in a dense web of connections that is difficult to interpret biologically. The MetNetGE application organizes and visualizes biological networks in a meaningful way to improve performance and biological interpretability.ResultsMetNetGE is an interactive visualization tool based on the Google Earth platform. MetNetGE features novel visualization techniques for pathway and ontology information display. Instead of simply showing hundreds of pathways in a complex graph, MetNetGE gives an overview of the network using the hierarchical pathway ontology using a novel layout, called the Enhanced Radial Space-Filling (ERSF) approach that allows the network to be summarized compactly. The non-tree edges in the pathway or gene ontology, which represent pathways or genes that belong to multiple categories, are linked using orbital connections in a third dimension. Biologists can easily identify highly activated pathways or gene ontology categories by mapping of summary experiment statistics such as coefficient of variation and overrepresentation values onto the visualization. After identifying such pathways, biologists can focus on the corresponding region to explore detailed pathway structure and experimental data in an aligned 3D tiered layout. In this paper, the use of MetNetGE is illustrated with pathway diagrams and data from E. coli and Arabidopsis.ConclusionsMetNetGE is a visualization tool that organizes biological networks according to a hierarchical ontology structure. The ERSF technique assigns attributes in 3D space, such as color, height, and transparency, to any ontological structure. For hierarchical data, the novel ERSF layout enables the user to identify pathways or categories that are differentially regulated in particular experiments. MetNetGE also displays complex biological pathway in an aligned 3D tiered layout for exploration.

Dataset Information

Interactive, multiscale navigation of large and complicated biological networks.

Motivation

Results

Availability

Contact

Supplementary information

Publications

Interactive, multiscale navigation of large and complicated biological networks.

Similar Datasets

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