Automatic layout and visualization of biclusters

Grothaus, Gregory A.; Mufti, Adeel; Murali, T. M.

Automatic layout and visualization of biclusters

dc.contributor.author	Grothaus, Gregory A.	en
dc.contributor.author	Mufti, Adeel	en
dc.contributor.author	Murali, T. M.	en
dc.contributor.department	Computer Science	en
dc.date.accessioned	2012-08-24T12:15:53Z	en
dc.date.available	2012-08-24T12:15:53Z	en
dc.date.issued	2006-09-04	en
dc.date.updated	2012-08-24T12:15:53Z	en
dc.description.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.	en
dc.description.version	Published version	en
dc.format.mimetype	application/pdf	en
dc.identifier.citation	Algorithms for Molecular Biology. 2006 Sep 04;1(1):15	en
dc.identifier.doi	https://doi.org/10.1186/1748-7188-1-15	en
dc.identifier.uri	http://hdl.handle.net/10919/18948	en
dc.language.iso	en	en
dc.rights	Creative Commons Attribution 4.0 International	en
dc.rights.holder	Gregory A Grothaus et al.; licensee BioMed Central Ltd.	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	en
dc.title	Automatic layout and visualization of biclusters	en
dc.title.serial	Algorithms for Molecular Biology	en
dc.type	Article - Refereed	en
dc.type.dcmitype	Text	en