Jurgelenaite Rasa, Dijkstra Tjeerd M H, Kocken Clemens H M, Heskes Tom
Institute for Computing and Information Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands.
Bioinformatics. 2009 Jun 15;25(12):1484-91. doi: 10.1093/bioinformatics/btp179. Epub 2009 Mar 31.
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.
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 data are available at Bioinformatics online.
迄今为止，对于恶性疟原虫生物学的一个基本过程，即包括转录控制在内的基因调控，我们了解甚少。我们使用噪声阈值模型来识别调控序列元件，这些元件解释了基因表达簇的成员身份，其中每个簇由在红细胞内发育周期的特定阶段活跃的基因组成。我们的方法既能捕捉基因调控的组合性质，又能纳入关于假定调控序列元件功能的不确定性。
我们发现了一种特征模式，即在周期前半段活跃的基因上游往往不存在最常见的基序，而在周期后半段活跃的基因上游则存在。我们没有发现证据表明基序的得分、方向、位置和多重性能改善基因表达的预测。通过比较基因组分析，我们找到了一份潜在转录因子及其相关基序的列表。
补充数据可在《生物信息学》在线获取。
