Gene regulation in the intraerythrocytic cycle of Plasmodium falciparum.
BACKGROUND
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.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Jurgelenaite
Rasa
R
Institute for Computing and Information Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands. r.jurgelenaite@cmbi.ru.nl
Dijkstra
Tjeerd M H
TM
Kocken
Clemens H M
CH
Heskes
Tom
T