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Publication year
2009Number of pages
8 p.
Source
Bioinformatics, 25, 12, (2009), pp. 1484-1491ISSN
Publication type
Article / Letter to editor

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Organization
CMBI
Data Science
Molecular Biology
Former Organization
Bioinformatics (umcn)
Journal title
Bioinformatics
Volume
vol. 25
Issue
iss. 12
Page start
p. 1484
Page end
p. 1491
Subject
Data Science; IGMD 8: Mitochondrial medicine; Molecular Biology; NCMLS 4: Energy and redox metabolismAbstract
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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
This item appears in the following Collection(s)
- Academic publications [205105]
- Electronic publications [103313]
- Faculty of Medical Sciences [81055]
- Faculty of Science [32348]
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