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Bioinformatics Advance Access originally published online on May 6, 2004
Bioinformatics 2004 20(16):2618-2625; doi:10.1093/bioinformatics/bth293
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Bioinformatics vol. 20 issue 16 © Oxford University Press 2004; all rights reserved.

GO-Mapper: functional analysis of gene expression data using the expression level as a score to evaluate Gene Ontology terms

Marcel Smid and Lambert C. J. Dorssers *

Department of Pathology, Josephine Nefkens Institute, Erasmus MC, P.O. Box 1738, 3000DR Rotterdam, The Netherlands

Received on January 23, 2004; revised on February 20, 2004; accepted on April 19, 2004
Advance Access Publication May 6, 2004

Motivation: Retrieval of information on biological processes from large-scale expression data is still a time-consuming task. An automated analysis utilizing all expression information would greatly increase our understanding of the samples under study.

Results: We describe here a novel method to obtain a functional analysis of complex gene expression data. Instead of applying a predefined expression threshold, Gene Ontology (GO) terms are weighted using the actual measured levels of expression of all associated genes. Based on this concept, the application GO-Mapper was developed to quantitatively link gene expression levels to GO-terms for multiple experiments in an automated way. The applicability of GO-Mapper was developed and validated on in house and public human microarray data and mouse SAGE data. We demonstrate that the GO-Mapper allows for interrelating relevant biological functions with the experiments under study.

Availability: The GO-Mapper application is free of charge available from our website.

Supplementary information: http://www.erasmusmc.nl/gatcplatform

Contact: l.dorssers{at}erasmusmc.nl

* To whom correspondence should be addressed.


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