Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum

R Jurgelenaite, T.M.H. Dijkstra, C.M.H Cocken, T. Heskes

Research output: Contribution to journalArticleAcademicpeer-review

11 Citations (Scopus)

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 the 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.
Original languageEnglish
Pages (from-to)1484-1491
Number of pages8
JournalBioinformatics
Volume25
Issue number12
DOIs
Publication statusPublished - 2009

Fingerprint

Gene Regulation
Plasmodium falciparum
Gene expression
Genes
Gene
Cycle
Gene Expression
Multigene Family
Threshold Model
Red Blood Cells
Transcription Factor
Transcription factors
Biology
Multiplicity
Genome
Tend
Uncertainty
Blood
Transcription Factors
Erythrocytes

Cite this

Jurgelenaite, R., Dijkstra, T. M. H., Cocken, C. M. H., & Heskes, T. (2009). Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum. Bioinformatics, 25(12), 1484-1491. https://doi.org/10.1093/bioinformatics/btp179
Jurgelenaite, R ; Dijkstra, T.M.H. ; Cocken, C.M.H ; Heskes, T. / Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum. In: Bioinformatics. 2009 ; Vol. 25, No. 12. pp. 1484-1491.
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Jurgelenaite, R, Dijkstra, TMH, Cocken, CMH & Heskes, T 2009, 'Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum', Bioinformatics, vol. 25, no. 12, pp. 1484-1491. https://doi.org/10.1093/bioinformatics/btp179

Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum. / Jurgelenaite, R; Dijkstra, T.M.H.; Cocken, C.M.H; Heskes, T.

In: Bioinformatics, Vol. 25, No. 12, 2009, p. 1484-1491.

Research output: Contribution to journalArticleAcademicpeer-review

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T1 - Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum

AU - Jurgelenaite, R

AU - Dijkstra, T.M.H.

AU - Cocken, C.M.H

AU - Heskes, T.

PY - 2009

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