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BMC Research Notes

, 2:124

First Online: 07 July 2009Received: 24 March 2009Accepted: 07 July 2009DOI: 10.1186-1756-0500-2-124

Cite this article as: Gonçalves, J.P., Madeira, S.C. & Oliveira, A.L. BMC Res Notes 2009 2: 124. doi:10.1186-1756-0500-2-124

Abstract

BackgroundThe ability to monitor changes in expression patterns over time, and to observe the emergence of coherent temporal responses using expression time series, is critical to advance our understanding of complex biological processes. Biclustering has been recognized as an effective method for discovering local temporal expression patterns and unraveling potential regulatory mechanisms. The general biclustering problem is NP-hard. In the case of time series this problem is tractable, and efficient algorithms can be used. However, there is still a need for specialized applications able to take advantage of the temporal properties inherent to expression time series, both from a computational and a biological perspective.

FindingsBiGGEsTS makes available state-of-the-art biclustering algorithms for analyzing expression time series. Gene Ontology GO annotations are used to assess the biological relevance of the biclusters. Methods for preprocessing expression time series and post-processing results are also included. The analysis is additionally supported by a visualization module capable of displaying informative representations of the data, including heatmaps, dendrograms, expression charts and graphs of enriched GO terms.

ConclusionBiGGEsTS is a free open source graphical software tool for revealing local coexpression of genes in specific intervals of time, while integrating meaningful information on gene annotations. It is freely available at: http:-kdbio.inesc-id.pt-software-biggests. We present a case study on the discovery of transcriptional regulatory modules in the response of Saccharomyces cerevisiae to heat stress.

Electronic supplementary materialThe online version of this article doi:10.1186-1756-0500-2-124 contains supplementary material, which is available to authorized users.

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Autor: Joana P Gonçalves - Sara C Madeira - Arlindo L Oliveira

Fuente: https://link.springer.com/







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