Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum

• Published in: Bioinformatics 2009-06, Vol.25 (12), p.1484-1491
• Main Authors: Jurgelenaite, Rasa, Dijkstra, Tjeerd M. H., Kocken, Clemens H. M., Heskes, Tom
• Format: Article
• Language: English
• Subjects: Animals; Biological and medical sciences; Computational Biology - methods; DNA, Protozoan - chemistry; Erythrocytes - parasitology; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling - methods; Gene Expression Regulation; General aspects; Genome, Protozoan; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Plasmodium falciparum; Plasmodium falciparum - genetics; Transcription Factors - genetics
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btp179

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. Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.