Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources

Blom, E.J., Breitling, R. , Hofstede, K.J., Roerdink, J.B.T.M., van Hijum, S.A.F.T. and Kuipers, O.P. (2008) Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources. BMC Genomics, 9, p. 945. (doi: 10.1186/1471-2164-9-495)

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Publisher's URL: http://dx.doi.org/10.1186/1471-2164-9-495

Abstract

Background: Despite a plethora of functional genomic efforts, the function of many genes in sequenced genomes remains unknown. The increasing amount of microarray data for many species allows employing the guilt-by-association principle to predict function on a large scale: genes exhibiting similar expression patterns are more likely to participate in shared biological processes. Results: We developed Prosecutor, an application that enables researchers to rapidly infer gene function based on available gene expression data and functional annotations. Our parameter-free functional prediction method uses a sensitive algorithm to achieve a high association rate of linking genes with unknown function to annotated genes. Furthermore, Prosecutor utilizes additional biological information such as genomic context and known regulatory mechanisms that are specific for prokaryotes. We analyzed publicly available transcriptome data sets and used literature sources to validate putative functions suggested by Prosecutor. We supply the complete results of our analysis for II prokaryotic organisms on a dedicated website. Conclusion: The Prosecutor software and supplementary datasets available at http://www.prosecutor.nl allow researchers working on any of the analyzed organisms to quickly identify the putative functions of their genes of interest. A de novo analysis allows new organisms to be studied.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Breitling, Professor Rainer
Authors: Blom, E.J., Breitling, R., Hofstede, K.J., Roerdink, J.B.T.M., van Hijum, S.A.F.T., and Kuipers, O.P.
Subjects:Q Science > QH Natural history > QH426 Genetics
College/School:College of Medical Veterinary and Life Sciences > School of Molecular Biosciences
Journal Name:BMC Genomics
Publisher:BioMed Central
ISSN (Online):1471-2164
Published Online:21 October 2008
Copyright Holders:Copyright © 2008 BioMed Central
First Published:First published in BMC Genomics 9:945
Publisher Policy:Reproduced in accordance with the copyright policy of the publisher.

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