Open Access Software

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

Evert Jan Blom1, Rainer Breitling2, Klaas Jan Hofstede1, Jos BTM Roerdink3, Sacha AFT van Hijum14 and Oscar P Kuipers1*

Author Affiliations

1 Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands

2 Groningen Bioinformatics Centre, University of Groningen Kerklaan 30, 9751 NN, Haren, the Netherlands

3 Institute for Mathematics and Computing Science, University of Groningen, Nijenborgh 9, 9747 AG, Groningen, the Netherlands

4 Current address: NIZO Food Research, Kernhemseweg 2, 6718 ZB, Ede the Netherlands

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BMC Genomics 2008, 9:495  doi:10.1186/1471-2164-9-495

Published: 21 October 2008



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.


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 11 prokaryotic organisms on a dedicated website.


The Prosecutor software and supplementary datasets available at webcite 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.