Research

Automatic layout and visualization of biclusters

Gregory A Grothaus^1,2 , Adeel Mufti¹ and TM Murali¹

¹  Department of Computer Science, 660 McBryde Hall, Virginia Polytechnic Institute and State University, Blacksburg VA 24061, USA

²  Google Inc., 1600 Amphitheater Parkway, Mountain View CA 94043, USA

author email corresponding author email

Algorithms for Molecular Biology 2006, 1:15doi:10.1186/1748-7188-1-15

Published:	4 September 2006

Abstract

Background

Biclustering has emerged as a powerful algorithmic tool for analyzing measurements of gene expression. A number of different methods have emerged for computing biclusters in gene expression data. Many of these algorithms may output a very large number of biclusters with varying degrees of overlap. There are no systematic methods that create a two-dimensional layout of the computed biclusters and display overlaps between them.

Results

We develop a novel algorithm for laying out biclusters in a two-dimensional matrix whose rows (respectively, columns) are rows (respectively, columns) of the original dataset. We display each bicluster as a contiguous submatrix in the layout. We allow the layout to have repeated rows and/or columns from the original matrix as required, but we seek a layout of the smallest size. We also develop a web-based search interface for the user to query the genes and samples of interest and visualise the layout of biclusters matching the queries.

Conclusion

We demonstrate the usefulness of our approach on gene expression data for two types of leukaemia and on protein-DNA binding data for two growth conditions in Saccharomyces cerevisiae. The software implementing the layout algorithm is available at http://bioinformatics.cs.vt.edu/~murali/papers/bivoc webcite.