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Bioinformatics Advance Access published online on March 31, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp179
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Gene Regulation in the Intraerythrocytic Cycle of Plasmodium Falciparum

Rasa Jurgelenaite 1,*,{dagger}, Tjeerd M.H. Dijkstra 1, Clemens H.M. Kocken 2 and Tom Heskes 1

1Institute for Computing and Information Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands,
2Department of Parasitology, Biomedical Primate Research Center, Rijswijk, The Netherlands

*To whom correspondence should be addressed. Ms. Rasa Jurgelenaite, E-mail: R.Jurgelenaite{at}cmbi.ru.nl


  Abstract

Motivation: To date, there is little knowledge about one of the processes fundamental to the biology of Plasmodium falciparum, gene regulation including transcriptional control. We use noisy threshold models to identify regulatory sequence elements explaining membership to a gene expression cluster where each cluster consists of genes active during part of the developmental cycle inside a red blood cell. Our approach is both able to capture the combinatorial nature of gene regulation and to incorporate uncertainty about the functionality of putative regulatory sequence elements.

Results: We find a characteristic pattern where the most common motifs tend to be absent upstream of genes active in the first half of the cycle and present upstream of genes active in the second half. We find no evidence that motif's score, orientation, location and multiplicity improves prediction of gene expression. Through comparative genome analysis, we find a list of potential transcription factors and their associated motifs.

Contact: R.Jurgelenaite{at}cmbi.ru.nl

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger}Current address: Center for Molecular and Biomolecular Informatics,Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands

Associate Editor: Prof. Martin Bishop

Received on December 2, 2008; revised on March 26, 2009; accepted on March 26, 2009

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