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Open Access Methodology article

Biclustering for the comprehensive search of correlated gene expression patterns using clustered seed expansion

Taegyun Yun1 and Gwan-Su Yi12*

Author affiliations

1 Department of Information and Communications Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea

2 Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea

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Citation and License

BMC Genomics 2013, 14:144  doi:10.1186/1471-2164-14-144

Published: 5 March 2013

Abstract

Background

In a functional analysis of gene expression data, biclustering method can give crucial information by showing correlated gene expression patterns under a subset of conditions. However, conventional biclustering algorithms still have some limitations to show comprehensive and stable outputs.

Results

We propose a novel biclustering approach called “BIclustering by Correlated and Large number of Individual Clustered seeds (BICLIC)” to find comprehensive sets of correlated expression patterns in biclusters using clustered seeds and their expansion with correlation of gene expression. BICLIC outperformed competing biclustering algorithms by completely recovering implanted biclusters in simulated datasets with various types of correlated patterns: shifting, scaling, and shifting-scaling. Furthermore, in a real yeast microarray dataset and a lung cancer microarray dataset, BICLIC found more comprehensive sets of biclusters that are significantly enriched to more diverse sets of biological terms than those of other competing biclustering algorithms.

Conclusions

BICLIC provides significant benefits in finding comprehensive sets of correlated patterns and their functional implications from a gene expression dataset.