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Open Access Highly Accessed Methodology article

On finding bicliques in bipartite graphs: a novel algorithm and its application to the integration of diverse biological data types

Yun Zhang1, Charles A Phillips2, Gary L Rogers2, Erich J Baker3, Elissa J Chesler4 and Michael A Langston2*

Author Affiliations

1 Dupont Pioneer, Johnston, IA 50131, USA

2 Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN 37996, USA

3 Department of Computer Science, Baylor University, Waco, TX 76798, USA

4 The Jackson Laboratory, Bar Harbor, ME 04609, USA

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BMC Bioinformatics 2014, 15:110  doi:10.1186/1471-2105-15-110

Published: 15 April 2014

Abstract

Background

Integrating and analyzing heterogeneous genome-scale data is a huge algorithmic challenge for modern systems biology. Bipartite graphs can be useful for representing relationships across pairs of disparate data types, with the interpretation of these relationships accomplished through an enumeration of maximal bicliques. Most previously-known techniques are generally ill-suited to this foundational task, because they are relatively inefficient and without effective scaling. In this paper, a powerful new algorithm is described that produces all maximal bicliques in a bipartite graph. Unlike most previous approaches, the new method neither places undue restrictions on its input nor inflates the problem size. Efficiency is achieved through an innovative exploitation of bipartite graph structure, and through computational reductions that rapidly eliminate non-maximal candidates from the search space. An iterative selection of vertices for consideration based on non-decreasing common neighborhood sizes boosts efficiency and leads to more balanced recursion trees.

Results

The new technique is implemented and compared to previously published approaches from graph theory and data mining. Formal time and space bounds are derived. Experiments are performed on both random graphs and graphs constructed from functional genomics data. It is shown that the new method substantially outperforms the best previous alternatives.

Conclusions

The new method is streamlined, efficient, and particularly well-suited to the study of huge and diverse biological data. A robust implementation has been incorporated into GeneWeaver, an online tool for integrating and analyzing functional genomics experiments, available at http://geneweaver.org webcite. The enormous increase in scalability it provides empowers users to study complex and previously unassailable gene-set associations between genes and their biological functions in a hierarchical fashion and on a genome-wide scale. This practical computational resource is adaptable to almost any applications environment in which bipartite graphs can be used to model relationships between pairs of heterogeneous entities.

Keywords:
Biclique; Biclustering; Bioinformatics databases; Bipartite graphs; Graph algorithms